The Pentagon yesterday withheld a $2 million payment to the Republic of the Marshall Islands for this year's rental of Kwajalein Atoll as a missile test site, contending that hundreds of demonstrators camping on atoll islands prevent its "unencumbered use," according to Assistant Secretary of Defense Noel Koch.

Although the United States has no plans to halt missile test flights aimed at Kwajalein lagoon and monitored by the radar on surrounding islands, Koch said the Marshallese government was "not maintaining the rental agreement," which requires the atoll to be available to the United States "in good order."

The demonstrators, representing some Kwajalein land owners, are protesting an agreement reached last month between the island government and the United States that calls for an annual payment of $9 million and runs for 50 years.

By holding back the money, the United States is attempting to put pressure on Marshall Islands President Amata Kabua to bring an end to the protests. Last month, Kabua's representatives completed negotiations on a new compact of association with the United States that would end the islands' trustee status, which has been in effect since World War II.

For the last 10 days, Kabua has been on Kwajalein trying to get individual land owners to sign his agreement and desert the protesters. Although U.S. government sources report that he has been convincing more each day, a lawyer for the land owners said yesterday he still has only a minority.

The Kwajalein Atoll Corp., which represents most of the land owners, has up to now made the atoll land available for the missile test range through an interim rental agreement with their own Marshall Islands government. The Pentagon paid the government and passed most of the money to the land owners, keeping some for public works projects on Kwajalein.

That agreement ran out last September, and the Kwajalein land owners' group has since sought to increase the rental fee to $16 million.

The Kwajalein lawyer said yesterday his group would probably file an action in the U.S. Court of Claims to force the government to pay.

The land owners have also announced an election in August, giving the residents an opportunity to say whether they want missile testing continued.

American officials said last week that such a "straw vote" would have no effect on U.S. intentions. As an indication of Kwajalein's importance, the first MX missile tests are due to be launched from Vandenberg Air Force Base, Calif., in January aimed at the lagoon.

The Kwajalein rental agreement is one of several controversial parts of the Marshalls compact. Another section calls for a $100 million U.S. payment, in return for which the Kabua government would take over and pay off all the thousands of claims for personal and property damage that arose out of American nuclear tests on Marshall atolls between 1946 and 1963.