"The best indication of United States' support to a particular terrorist group is that one of the leaders of this terrorist group was given the opportunity to speak on VoA [Voice of America radio station] after committing the crime," Haddadadel said.
"There is no news, no evidence, and we don't have any reason to believe that the military establishment in Pakistan is also supporting such militant groups."
ABC News, citing US and Pakistani intelligence sources, said the raids had resulted in the deaths and capture of Iranian soldiers and officials.
The group, called Jundullah and made up of members of the Baluchi ethnic group, who live in Pakistan and Iran, operated from the Baluchistan province, the report said.
The group said it carried out an attack in February that killed at least 11 members of the Iranian Revolutionary Guard on a bus in the Iranian city of Zehedan.
ABC reported Pakistani government sources as saying the secret campaign against Iran was on the agenda when Dick Cheney, the US vice president, met Pervez Musharraf, the Pakistani president, in February.
The Pakistani foreign ministry dismissed the ABC report as "tendentious". It said the suggestion that Pakistan was involved in a secret war against Iran was "an absurd and sinister insinuation".
Haddadadel said on Thursday that Iran had to step up co-operation with Pakistan on the border.
"Some of the militants, the rebel forces are active in our border areas and we should work with Pakistan in order to increase security co-operation," he said.