The Navy tested a version of its controversial new submarine-launched Trident II missile that can carry 12 warheads two months ago, according to a staff working paper released yesterday by the Congressional Budget Office.

Senate and House critics have said they thought that the first test flight of the 12-warhead model was to take place Nov. 5. That one was delayed.

Instead, the CBO study said that on the sixth flight test of the Trident II two months ago, the missile carried a device capable of delivering 12 warheads, although only 10 of the so-called "stations" on the vehicle were used.

The congressional critics have said they believe that this version of the missile could affect U.S. strategic-force levels and complicate arms-control negotiations with the Soviet Union.

At issue is whether the Trident

II will be counted under a future arms agreement with the Soviets

as carrying 12 warheads, or

only eight, the number on the already-tested version of the mis- sile.

Under counting rules of the unratified 1979 SALT II treaty, the number of warheads carried by all missiles of one type is to be the largest amount flight-tested on that type.

The CBO study concluded, as had House and Senate critics, that continued testing of the missile with 12 warheads "could make negotiations more difficult" because it would be "hard to get the Soviet Union to accept" an agreement stating that the Trident has only eight warheads.

The next test was supposed to carry the full load of 12 dummy warheads, CBO said.

Defense Secretary Caspar W. Weinberger supported the 12-warhead test during interagency discussions last summer despite objections from State Department officials who expressed concern about its impact on arms negotiations.

Weinberger argued that the administration was no longer abiding by SALT II.

However, some ranking Navy officers reportedly oppose the 12-warhead version because it could limit the size of the strategic submarine force if a future arms agreement meets the lines of current discussions calling for a 50 percent reduction in U.S. and Soviet strategic warheads.

The Navy said it postponed the Nov. 5 test for a week because it would have occurred on the same day that Weinberger's resignation was announced by President Reagan.

Although Weinberger had actively promoted the test, Defense Department officials decided to delay it because of possible adverse publicity.

The firing was put off a second time last week because Senate Armed Services Committee Chairman Sam Nunn (D-Ga.), responding to colleagues' requests, demanded a hearing with Pentagon witnesses to justify the test before it took place.

Nunn threatened to delay last Thursday's confirmation hearing on Weinberger's proposed successor, Frank C. Carlucci, if necessary to obtain a postponement of the test, according to a senator involved in the matter.

The hearing with Pentagon witnesses may be scheduled soon, a Nunn aide said yesterday. Nunn expects to have Navy officials and a representative of the Joint Chiefs of Staff at his planned hearing along with Weinberger, if he wants to appear, a committee aide said.