Why were the Israelites not circumcised in the desert?

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Keil explains it well:

The sentence upon the fathers, that their bodies should fall in the desert, was unquestionably a rejection of them on the part of God, an abrogation of the covenant with them. This punishment was also to be borne by their sons; and hence the reason why those who were born in the desert by the way were not circumcised. (Commentary on the Old Testament by C. F. Keil)

As the covenant of the Lord with the fathers was broken, the sons of the rejected generation were not to receive the covenant sign of circumcision. This curse upon the fathers, casting some shame upon the children for a period seems more like probation. As far as the nation as a whole was concerned the covenant was not fully collapsed. Only until the generation of men that were capable of bearing arms when they came out of Egypt were all dead would the younger generation which had grown up in the desert be under the shame. When the time of punishment was over and the temporary suspension of the covenant passed, it was a good time to renew the terms of the covenant with a new generation.

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While the quote from Keil's Commentary has merit, I would modify and expand it slightly.

This is the quote: The sentence upon the fathers, that their bodies should fall in the desert, was unquestionably a rejection of them on the part of God, an abrogation of the covenant with them. This punishment was also to be borne by their sons; and hence the reason why those who were born in the desert by the way were not circumcised. (Commentary on the Old Testament by C. F. Keil)

The rejection of the mature, however, came before the Law of Moses was issued. In Exodus 19 Israel is offered the Covenant of Abraham, which according to Galatians 3 was 430 years prior and was spoken to all Israel by God. (Gen 26:5) They were offered the opportunity to be a "peculiar treasure...a kingdom of priests and a holy nation" (Ex 19:5-6) They said "All that the Lord has spoken will we do..."(v8) This was not, however, from their heart. (Deut 5:29) Remember, though they were circumcised in Egypt, they had been in a pagan society for 400 years(ish) and they brought that evil with them. Remember the golden calf.

This promise of kingdom of priests was not fulfilled until Christ confirmed the covenant of Abraham, and it became called the New Covenant because it caused the Mosaic Covenant to become the Old Covenant, (Heb 8:13) and because Jesus' blood finalized and confirmed the blood Covenant between God and Abraham. (Gal 3 et. al.) (God's blood in Christ was the completion of the substitutionary blood of the animals in the cutting of the Covenant with Abraham, and Abraham's blood was shed in circumcision, when the blood was shed, physical circumcision is not longer necessary.) This rejection of the Covenant of Abraham and the voice of God speaking the terms of the Covenant from Mt. Sinai caused God to reject the mature, disallowing them to exercise circumcision, the sign of the covenant they had rejected upon their children. The children were circumcised later by Joshua upon the end of the 40 years and the death of those who had rejected God's direct relationship as opposed to relationship through the mediation of Moses and the priests of Levi.

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