Here is an answer based on my experience at the beginning of September 2022.

I’m an Australian citizen and we are also allowed to stay in Malaysia for 90 days.

Some countries make a distinction between "visa waiver" and "visa free" entry I believe. I know I’m here on a "visa free" basis. This may make a difference. Also of course having a normal visa could also mean different rules.

I was planning to leave Malaysia a few days before my 90 days were up but misremembered my date of arrival. When I checked my passport stamp I realized I was already on day 89 so decided I better leave that day. I considered the ferry to Batam, Indonesia since I was in Johor Bahru, but I wasn’t sure of the covid rules for Indonesia regarding quarantine and insurance whereas I had come to JB from Singapore and knew I would be fine to return to Singapore. But school holidays had just begun and the budget accommodation was sold out for at least ten days. Which meant I would have to return to Malaysia the same day or next day. Not ideal but the staff at my guesthouse thought it should be fine.

I entered Singapore about 8.30pm and walked a couple of km to find a 24-hour coffeeshop with Wi-Fi and aircon where I stayed until about 1.30am before walking back to the causeway.

The immigration officer gave me a new 90-day stamp, but the new stamp has a small circle around the "90" drawn in pencil. He did not ask me any specific questions or give me any warnings.

I assume the circle is a type of code for the next immigration officer and that that officer will take into account the fact that I maxed out my first 90 days and then did a "U-turn". No doubt they will also take into account how much of this next 90 days I use up before leaving.

So it seems one visa run is OK but they are aware of what you’re doing and are keeping an eye on your movements in and out of the country. What type of visa or visaless entry you’re on may make a difference, as may the country you’re from. It’s also possible it’s easier at the moment because Johor at least has suffered greatly economically while the causeway to Singapore was closed. I think the officer assesses the likelihood that a visitor may have been working while on a tourist entry and whether they’re likely to be spending much in the local economy.

A lot of this is guesswork of course. I’ll add photos of my passport stamps later.

I would not try doing a "U turn" visa run twice. Leaving for a month or longer before coming back and leaving well before the end of the 90 days is surely a safer bet.

US Citizen

1. You can apply for an extension of stay before your Visit Pass Expires (at least 5 working days) by providing valid reasons. Most probably you can be given once (only) an extension of 2 months.

2. You can perform a “visa run” only once w.e.f. from 2019 onwards. You have to leave Malaysia for at least 5-7 days, only re-entry can be accepted, but the immigration can restrict the period of stay to less than 90 days. It is at the discretion of the IMI Officer attending to you.

3. From 2020. there are more changes in Immigration Controls to combat human trafficking and illegal immigration. There should be more announcements very soon throughout the world. US, UK, EU, ASEAN countries.

4. Overstay even 1 day is overstay under Malaysian Immigration and Civil Laws. It is a Criminal Offense unless there are material changes in 2020.

5. For more constructive and up to date information on overstay issues and/or “Deny Entry” issues, you may access this Free Legal Malaysian Website : https://www.lawyerment.com/answers/questions/13181/what-to-do-if-you-overstayed-in-malaysia-updated-with-policies-wef-01-01-2019

6. You may also ask Dr. Google by asking “overstay in Malaysia”.

If it’s the first time you do this then you won’t have problems. However if you do it regularly and have been in Malaysia many times before then they may look a little closer. I would also take a cheap Air Asia flight and stay out of the country for at least a couple days if you want to be totally sure.

It is definitely risky. I know a few people who did that successfully a couple of years ago and I know a person who was detained in a cell for a night and then got deported.

Usually it’s pretty obvious to the immigration that you are doing a visa run, and most likely they will question you about it. For it to be successful the officer has to be convinced that you are genuine tourist and you don’t work or study in Malaysia.

You can only do this for one time. Most likely if you repeat, they’ll either deport you or give you a short visa.

Here’s some things you can do:

• Immigration is more strict if you travel by land or sea. I’d suggest flying to Singapore or Indonesia.
• Make sure it is at least 5 days. I’ve heard shorter trips are much more risky.
• A different port of entry, for example Langkawi might help. In case if they asked why you are returning tell them I am tired of Kuala Lumpur.
• Have a return ticket that is slightly more than 2 months. Note that shorter return ticket might help you but they might give you shorter visa too.
• Book a hotel, there are cheap hotels which only charge the first night on the event of no-show. You can book them from hotel booking websites without debit/credit card.
• When returning, at the immigration, try to choose an officer that is smiling!

On the other hand, you can also register at one of the language schools and get a 6 months legit student visa and you’ll have the added benefit of the learning a new language. Note that you might be required to go back to your country and come back since 2 years ago there was a law that you couldn’t convert social pass to student visa. It might have been changed now. Also you need at least 80% attendance of the classes.

Given that you apparently wish to stay in Malaysia for 180+ days I have serious doubts that you are a genuine tourist / business traveler and any immigration official is able to make similar conclusions. They will then go on to ask whether you are living in Malaysia illegally and whether you are working there off-the-books.

I have found two recent articles from 2013 and 2015 that describe that Malaysia (like Thailand) is now clamping down on visa runs. The rule of thumb apparently is that you are in trouble if “the passport shows more than three exit and returns within a short period of time.” as stated in both articles but even your first visa run could give you trouble.

The more recent article talks of a Swiss couple being detained for two days in a not-to-land room (read: prison cell) and then released with only a one-week visa following public pressure after their case got to the press.

The older article links the practice of visa-runs explicitly to drug trafficking and prostitution which may give you an idea why it is not kindly looked upon by officials.
A comment of 2014 there also supports that immigration is sensitive to the issue:

My husband and I who are retired just made our very first visa run after having the last three months in Penag. We flew to singapore for four days. Upon arriving back in Penag we were hassled by immigration and reluctantly given another 90 days but told we had to apply for the MM2H visa. We told them we were seeing if we like Malaysia before we made such a big commitment as it involved moving 50,000 into a malaysian bank account. Immigration didn’t care.

@pnuts has posted this link to a LP forum in comments where plenty of people suggest a visa run to Singapore. However the thread is four years old and cites personal experience dating from 1999! Do also note that the OP there in fact intends to do a visa extension in KL which is also my recommendation for you!