The bodies of Jaspal Singh and Mahal Singh were found in Khyber and Aurakzai regions Sunday after their relatives failed to pay a ransom allegedly demanded by Taliban. It is reportedly the first time a Sikh has been killed by militants in Pakistan.
The militants had demanded a ransom of 30 million rupees (£423,000) to be paid by February 20.
There are reports that the two Sikhs were beheaded after they refused to convert to Islam.
It is believed more members of the minority community are being held as captives.
Condemning the beheading, the Asia Evangelical Alliance – an association of evangelical bodies - called the Pakistani Government to ensure protection of minority groups in the country.
"AEA calls the Pakistani government to ensure the safe release of those still in the custody of militants," stated a release by general secretary of AEA, Rev Dr Richard Howell.
Howell appealed the government there to "make every effort to ensure the protection of minority groups, especially their right to religious freedom".
The Indian government has strongly condemned the "barbaric" beheadings and has sought the safety of all minorities in the country. The issue is likely to come up during the talks between the two countries, which start today.
Last year, Islamic militants in Khyber Agency imposed ‘jizya', or religious tax on Sikhs, Hindus and Christians. Those failing to make the payment have either had to convert to Islam or leave the tribal belt.
Khyber Agency is one of seven semi-autonomous tribal agencies along the Afghan border.