TEHRAN, Sept 4 (Reuters) - A senior Iranian official denied allegations that Iran has been shelling Kurdish areas in neighbouring Iraq, an Iranian news agency said on Tuesday.

Iraqi officials accused Iran last month of shelling Kurdish villages in Iraq's northeast, a move Iraqi Foreign Minister Hoshiyar Zebari said threatened ties with Iran.

An Iranian Foreign Ministry spokesman said on Sunday it would investigate reports of shelling in Kurdish areas in Iraq, in the first official comment from Tehran on the issue.

Iran's ISNA news agency said on Tuesday that Deputy Foreign Minister Mehdi Mostafavi had "denied any bombing of Iraq's northern border by Iran".

Cross-border clashes occasionally occur as Iran and Turkey battle Kurdish separatist rebels operating from bases in Iraq's mountainous northeastern region of Kurdistan.

Baghdad has said hundreds of people were evacuated from villages due to the shelling. Kurdish PJAK guerrillas, who seek autonomy for Kurdish areas in Iran, are believed to shelter in the area.

PJAK, the Party of Free Life of Kurdistan, is an Iranian offshoot of the Kurdistan Workers Party (PKK), a Kurdish separatist movement that is fighting Turkey.

"Some border problems between neighbouring countries naturally and predictably happen," ISNA quoted Mostafavi as saying.

"There are some armed terrorist groups who sometimes make some violations ... We strongly defend our borders and we don't let (anyone) penetrate," he added, remarks that echoed comments made by other officials.

Ties between Iran and Iraq, both mainly Shi'ite Muslim, have improved since 2003 when U.S. forces toppled Saddam Hussein, a Sunni Muslim who waged an eight-year war with Iran in the 1980s.

U.S. officials say Iran is fomenting violence inside Iraq. Nevertheless, U.S. and Iranian officials have held talks on Iraq in Baghdad since May, the most high profile meetings since ties were cut after the 1979 Islamic revolution.

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