THE REAGAN administration is in high dudgeon over the allegedly improper billings of General Dynamics, the country's largest defense contractor ($7 billion a year). The spokesman of the secretary of defense declares that the company's congressional testimony about some of its practices is "nauseating." The secretary himself announces, before the American Legion, a new policy requiring contractors to certify they are not asking the government to pay for political contributions, entertainment and the like.

To which we and, no doubt, many of you are compelled to say: Where on earth has the Pentagon leadership been for the last five years? How can it have been spending more than one trillion dollars in this time, promised at every turn to combat waste, fraud and abuse, and still failed to stop the sort of apparent derelictions -- like charging the government to keep an executive's dog in a kennel and to fly the company chairman to his family farm -- that are now in the news? The Pentagon's shock and sternness are marvelous to behold: some of General Dynamics' claims are pronounced "preposterous," and a "get-tough" policy is enunciated to deal with contractors from here on out. But where have these people been?

The "system," it is said, is flawed: the auditors may turn up the goods, but there is only a tenuous connection to the contracting people, who go ahead churning out the checks, and there is scarcely any connection at all to the political appointees, who are engaged in other things. This is why egregious contracting abuses are ignored -- true, they are not all ignored -- until there is a public fuss and the administration becomes frightened that Congress will be diverted by the smell of scandal into failing to see the urgency of voting for the defense budget. After all, insiders quietly assert, by Pentagon standards the money is only nickels and dimes.

It seems to us insupportable, nonetheless, to have tolerated these questionable practices -- by General Dynamics, by Boeing, which was most recently in the news for billing the Pentagon $127,000 for political contributions, by anyone. Secretary Weinberger has suspended a $40 million overhead payment to General Dynamics for 30 days. That's about one-half of one percent of its annual contracts.

Rep. John Dingell, whose investigations got this whole thing started, has suggested terminating General Dynamics' $5 billion attack submarine contract for violating a contractual provision barring gifts to government officials -- Adm. Rickover. We'd like to know the argument against it. We'd also like to know if there is any plausible explanation of why the Pentagon, with its army of auditors and contract officers and investigators of every kind should have discovered that things were "nauseating" only on March 6, 1985.