Jaspal Singh and Mahan Singh, both businessmen, were kidnapped from Tira Valley in Khyber agency and Darra Adamkheil in Orakzai agency on Jan 19.
The Sikhs were kidnapped 34 days ago and the Taliban had demanded Rs 30 million as ransom for their release.
According to sources, two of the kidnapped Sikhs were beheaded after the expiry of the deadline for the payment of the ransom.
Some more members of the minority community are still in the custody of the rebels.
The kidnapping took place in an area where there the government has virtually no control and the militants are in a dominant position.
Delhi Sikh Gurdwara Prabandhak Committee (DSGPC) condemned the incident and said that Pakistan government should take strong action against Taliban.