MANILA, Philippines (AP) _ A move in the Senate to ban nuclear weapons from the Philippines threatens to strain relations with America and will test President Corazon Aquino's relations with Congress.

Last week, 12 of the 24 senators co-sponsored legislation that would ban nuclear arms from Philippine territory and call for criminal penalties for those who import them and for officials who tolerate their presence.

Sponsors have said the bills were aimed specifically at nuclear weapons believed stored at the U.S. bases in the Philippines - Clark Air Base and the Subic Bay naval station. The United States refuses to confirm or deny the presence of nuclear weapons at overseas bases or aboard its warships.

If approved, the ban would be stricter than one imposed by New Zealand, which bars nuclear-armed ships from its ports but permits transit through its territorial waters. That decision, because of U.S. opposition, has virtually ended New Zealand's participation in the post-World War II ANZUS treaty between America, Australia and New Zealand. Last year, the United States suspended security commitments to New Zealand and reduced the exchange of intelligence information.

The Philippine measures would ban storage and import of nuclear arms ''into the country or within its territorial waters (and airspace).''

Both the Philippine and U.S. administrations clearly want to avoid friction over the issue, especially at a time when Mrs. Aquino's govewrnment is seeking more economic aid and military assistance to revive the economy and confront Communist rebels.

The rebels have been fighting the government for 18 years.

Mrs. Aquino has taken no public position on the nuclear issue.

U.S. State Department spokeswoman Phyllis Oakley refused comment last week, but noted the legislation would have to pass both the Philippine Senate and the more conservative House of Representatives.

The proposal has strong support in the Senate. Nearly half its members have gone on record as saying the U.S. bases are vestiges of American ''colonial'' rule and should be closed.

Co-sponsors of the anti-nuclear measure include Senate President Jovito Salonga and Sen. Agapito Aquino, Mrs. Aquino's brother-in-law.

The new Philippine constitution, ratified by a plebiscite last February, states: ''The Philippines, consistent with the national interest, adopts and pursues a policy of freedom from nuclear weapons in its territory.''

The constitutional commission approved the provision in September 1986 after rejecting a tougher proposal to declare the country a ''nuclear free zone.''

Last January, opposition politician Homobono Adaza released tape recordings he said were of a telephone conversation between Mrs. Aquino and aides in which they voiced concern over ramifications of the provision on U.S. bases.

According to the transcript, which Mrs. Aquino's staff never disavowed, Executive Secretary Joker Arroyo said the anti-nuclear provision would render the bases useless because ''the Americans will not care ... to maintain those bases if there are no nuclear weapons.''

Some presidential staff sources, speaking on condition they not be identified by name, maintain the constitutional provision is not a clear-cut ban because the government may consider the presence of such weapons ''consistent with the national interest.''

Political sources, demanding anonymity, say the president could lobby quietly to delay action on the anti-nuclear measure, while the Congress tackles other legislation or, if the measure is approved, use her veto.

But both moves would reinforce claims from the increasingly militant left that she is a ''puppet of the United States.'' That is a charge trade union and social activist groups are raising with greater frequency because of her commitment to foreign investment and to repaying the nation's $28 billion foreign debt.

It could also create problems in 1991 when, under the new constitution, two-thirds of the Senate must approve any extension of the U.S. bases.