Now it is the secretaries of the Army, Navy and Air Force who are complaining that President Carter's lid of 5.5 percent on government pay increases is unrealistically low.

The service secretaries, Defense Department officials confirmed yesterday, recently wrote letters to Defense Secretary Harold Brown contending that military people should not be held to the president's ceiling of 5.5 percent for government workers.

What's more, one high-ranking Pentagon official said, Brown agrees with that argument, especially in light of the fact that it is becoming increasinly difficult to recruit people for the military.

The Service secretaries argue that military pay raises should be at the 7 percent level suggested for private industry - not the 5.5 percent suggested for government employes. The White House has not responded to their complaints, according to Pentagon officials.

The Carter administration has directed that government pay increases be limited to 5.5 percent for fiscal 1979 and 1980.

In a separate development affecting future military pay, one Pentagon official predicted yesterday the people on active duty in the military will fare better than government civilians under the pay reforms the Carter administration unveiled Wednesday.

The reason for this prediction, the spokesman said, is that increases in military pay would be based in fiscal 1981 and beyond on the Bureau of Labor Statistics indices that are used now. Military benefits, such as retirement pay and medical care, would not be considered as a discount in figuring how large a pay increase the military should receive.

In contrast, for federal civilian workers fringe benefits such as retirement pay will be computed in arriving at pay increases designed to correspond to the compensation available in private industry for the same work.

While Pentagon executives insist that the president's reform pay proposals would not result in an overhaul of the military pay structure, they acknowledged this is not true of the reforms they have in mind for the military retirement system.

Any tinkering with military retirement, which is costing over $10 billion a year, is sure to draw emotional protests from service people. The Carter administration's reform package is nearly completed and will be made public soon, according to the Pentagon.

Congress must approve any major changes in military pay and retirement.