"All issues concerning the relations between the two countries, depending upon the time permitting, will be taken up for discussion," he said.
Foreign Secretary Nirupama Rao, too, has condemned the act.
Speaking on Sikhs beheading by Taliban, she said: "We seek more facts and terrorism will be part of upcoming Indo-Pak talks."
The shocking incident is said to have taken place in the restive North West Frontier Province (NWFP) of Pakistan.
According to sources in Indian government, the Sikhs - all of them Pakistani citizens - were beheaded and their heads were thrown into a common area to invoke fear among the locals. The body of Jaspal Singh was found in the Khyber tribal region, located a short distance from the provincial capital of Peshawar, while the body of Mahal Singh was found in the Aurakzai Agency, sources said.
There was some confusion about the total number of Sikhs who were kidnapped for ransom from the Bara area of Khyber Agency by the Tehrik-e-Taliban Pakistan. A source said four Sikhs were abducted while another report said the total number of kidnapped persons was six.
The Sikhs were kidnapped 34 days ago and the Taliban had demanded Rs 30 million as ransom for their release. Two of the kidnapped Sikhs were beheaded after the expiry of the deadline for the payment of the ransom, sources said.
Speaking to NDTV, a minister in the North West Frontier Province in Pakistan Bashir Ahmed said, "According to the information we have, three Sikhs were kidnapped by the Taliban in the Federally Administered Tribal Area (FATA). One of them was murdered by them and they sent his body to Peshawar."
He added: "The other two people are with Taliban and we are trying to contact them but they have not made any demand for the release of these people. We have been trying since the last 15 days, but they have never asked for money or any other demand."
Gurvinder Singh and Gurjit Singh are still in the custody of the militants, sources said. The kidnapping occurred in an area where there the government has virtually no control and the militants are in a dominant position, sources said.
An estimated 10,000 Sikhs lived in the NWFP and in the tribal belt, particularly Aurakzai Agency, till the Taliban imposed 'jizya' or religious tax on them last year. Most members of the community then fled to cities across Pakistan.
(With PTI inputs)