Confirming that his favoured candidate to become the next chief of joint staffs, General Joseph Ralston, committed adultery during his meteoric air force career, Mr Cohen said he had decided to stand by the general's candidacy.
In an interview published in the Washington Post, Mr Cohen - who has strongly defended the enforcement of rigorous moral standards in the armed forces through the past scandal-ridden weeks - said that it was time to draw the line. "We need to come back to a rule of reason instead of a rule of thumb."
General Ralston has admitted to having an affair with a CIA agent 13 years ago while separated from his wife. He is now divorced and remarried. Reporters investigating the case have established that the general did not inform his military superiors of the affair and it was never the subject of disciplinary action - although it was common knowledge among his colleagues, one of whom described it as "flagrant".
Mr Cohen, who described General Ralston's affair as "a human error" that was outweighed by his sterling 32-year record, admitted that the decision to stand by the general put him in "a very difficult situation".
The commander at a major army training centre and a director at the same establishment were forced into early retirement this week after admitting adulterous affairs in years gone by, and other senior officers are under investigation.
The previous week, in a highly publicised case, Lieutenant Kelly Flinn, the air force's first female B-52 bomber pilot was given a general discharge in lieu of court martial after admitting an affair with a married civilian and disobeying an order to break it off. Her lawyer claimed that the military observed double standards and tended to turn a blind eye to the sexual dalliances of senior (male) officers.
These cases came amid a spate of courts martial in which male officers are accused of sexually harassing female subordinates. Yesterday, an army sergeant at the US base at Darmstadt in Germany became the first US soldier serving outside America to be convicted of sex crimes, when he was sentenced to two years in prison for indecent assault and other offences.
The jury gave Davis a dishonourable discharge but cleared him of six rape charges, one count of sodomy and other assault charges brought forward by 15 current or former female soldiers. Prosecutors had asked for a minimum sentence of five years for Davies, whom they called a "sexual predator" who used his rank to get sex.
Davies told journalists that he felt betrayed by the army and also by US civil rights leaders, to whom he had appealed for help in the case. "Race was indeed an issue," Davies said. "This was a witch hunt."
Although Mr Cohen says hesupports General Ralston to succeed General John Shalikashvili when he retires as chief of the joint staffs in September, the candidates' list is not closed. The White House, perhaps sensing new political difficulty in the nomination, which must be approved by the Senate, said no final decision had been taken.