ISLAMABAD, Pakistan (AP) _ Two Afghan warplanes were hit over Pakistan by missiles fired by U.S.-made Pakistani F-16s and were believed to have been destroyed, the Defense Ministry said.

A ministry statement said the two planes were among six Afghan aircraft that intruded in Pakistani airspace with the aim of bombing targets here.

''Search for the wreckage is in progress for final confirmation (that the two planes were destroyed),'' the statement said, adding that all Pakistani planes returned safely.

The ministry said, ''Six Afghan aircraft on Monday violated the border of Pakistan, north of Nawagai in the North West Frontier province with the intent of bombing our territory.'' Nawagai is 120 miles northwest of Islamabad, and 12 miles from the Afghan border.

''Two Pakistan air force F-16 aircraft intercepted the raiders and engaged two of the Afghan aircraft with air-to-air missiles at high altitude.

''All video and electronic sensors on board the F-16s indicate positively that the two intruders were hit by missiles.''

The statement gave no further details.

Pakistan also claimed last Wednesday to have downed an intruding Afghan plane after several Afghan warplanes were engaged by Pakistani F-16s. The ministry also put the scene of the engagement then as Nawagai. But state-run Radio Kabul called the Pakistani claim ''baseless'' and ''a lie.'' It challenged Pakistan to produce the wreckage. Islamabad failed to do so.

If verified, the Wednesday and Monday claims would make a total of six warplanes shot down by Pakistan since the guerrilla war in Afghanistan began.

Those include a Soviet-piloted Su-25 warplane which Pakistan shot down over its territory Aug. 4. The Soviet pilot, Col. Alexander Vladimirovich Rudskoi, was captured, but was handed over to the Soviet Embassy in Islamabad on Aug. 17.

Relations between Islamabad and Kabul have suffered since late 1979, when Soviet troops marched into Afghanistan to support Afghanistan's pro-Moscow government. Thousands of anti-communist guerrillas have fought the Soviet troops and Afghan forces since then. Moscow and Kabul accuse Pakistan, the United States and China of aiding the guerrillas militarily.

Half of the 115,000 Soviet troops have left Afghanistan by the stipulated date of Aug. 15, under U.N.-brokered Geneva accords signed last April 14. The remaining troops are to leave by next Feb. 15.

Pakistan, Afghanistan, the United States and the Soviet Union signed the accords as a step toward bringing peace in Afghanistan.

Earlier Monday, guerrillas were reported to have taken two key border garrisons in southeastern Afghanistan in a series of communist defeats there. Guerrillas and Western diplomatic sounces said the Kabul government moved thousands of troops to the provincial capital of Kandahar to shore up defenses sagging from weeks of guerrilla onslaughts.

''Reports we have received concerning the regime's situation in (southeastern) Afghanistan indicate that the position of the regime is deteriorating,'' said one Western diplomatic source in Islamabad.

The sources spoke on the condition of anonymity.

Kandahar has long been seen as a key element in the insurgents' drive to capture provincial capitals as Soviet forces withdraw.

The guerrillas claim they overran the border garrison of Spin Boldak after a two-month siege last Friday, capturing many weapons and large amounts of ammunition.

The following day, guerrillas claimed a similar victory farther up the border at Khair Kot in Paktika province, also a key supply route.

The guerrillas, known as mujahedeen, or holy warriors, reject all offers for a political settlement with the communists. They have taken two provincial capitals this summer: Talogan in the north and Bamyan west of Kabul. They also briefly held the key northern city of Kunduz before heavy Soviet aerial bombardment forced them to flee.

The guerrillas also repeatedly penetrated Kabul's fortress-like defenses to launch a series of blistering rocket attacks in recent weeks.

On Sunday, a large car bomb exploded on a main shopping street near the Pakistan Embassy, killing 10 people and wounding about 40.