(Adds 10 militants captured, explosives found in Swat)

By Robert Birsel

ISLAMABAD, Jan 19 (Reuters) - Pakistani forces captured 40 militants in the South Waziristan region on the Afghan border, a military spokesman said on Saturday, a day after up to 90 rebels were killed in two battles.

Fighting has intensified in recent days between government forces and al Qaeda-linked militants led by a commander the government and the CIA say was behind the assassination of opposition leader Benazir Bhutto last month.

"Last night, during the operation at Chaghmalai, we captured 40 miscreants ... the complete Chaghmalai area is cleared of militants," said military spokesman Major-General Athar Abbas.

A wave of violence including a barrage of suicide bombs in recent months has raised fears about stability in nuclear-armed Pakistan, which is a major ally of the United States in its campaign against terrorism.

The assassination of two-time prime minister Bhutto in a gun and bomb attack in Rawalpindi on Dec. 27 compounded that worry.

Militants ambushed a convoy in the Chaghmalai area of South Waziristan on Friday and 20 to 30 of them were killed when security forces fought back, Abbas said, citing estimates reported by observation posts.

The military later found the bodies of 10 fighters, he said.

In another incident on Friday, government forces attacked a large number of men who had gathered to attack a fort at Ladha, also in South Waziristan, killing 50 to 60 of them, Abbas said.

Intense fighting continued through the night at Ladha, he said, and locals said aircraft bombed militants on Saturday.

In a separate incident, security forces said they arrested 10 militants and found 2.5 tonnes of explosives hidden in a mosque in the Swat valley in North West Frontier Province, where the army has been battling Islamists since November.

SEARCH FOR MISSING

The government said al Qaeda-linked militant leader Baitullah Mehsud, who is based in South Waziristan, was behind Bhutto's killing.

CIA Director Michael Hayden, in an interview with the Washington Post published on Friday, also blamed Mehsud for Bhutto's murder.

The government says the militants are intent on destabilising the country. A spokesman for Mehsud, who earlier denied the commander was behind Bhutto's killing, was not immediately available for comment on the latest clashes.

Security forces have been battling al Qaeda-linked militants in South Waziristan for several years. The mountainous region, occupied by conservative, independent-minded Pashtun tribesmen, has never come under the full authority of any government.

Militants flocked to Waziristan and other areas on the Afghan border in the 1980s to support U.S.- and Saudi Arabian-backed Afghan guerrillas fighting Soviet troops in Afghanistan.

Many al Qaeda and Taliban members took refuge on the Pakistani side of the border after U.S.-led troops ousted the Taliban government in Afghanistan weeks after the Sept. 11, 2001, attacks on the United States.

Hundreds of militants overran a paramilitary fort in another part of South Waziristan on Wednesday. Government forces were still searching for 18 paramilitary soldiers who went missing during that attack, Abbas said. (Editing by Matthew Jones)

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