His statement came after the GMB union claimed that up to 70 people who worked at the nuclear facility may have had tissue, bones and other body parts removed without the knowledge of their families.
Mr Darling said that BNFL had told him that in 65 cases tissue was taken from individuals and analysed for radioactivity.
However the surviving records only show what was removed at post-mortem. They do not indicate who asked for an examination or under what authority or for what purpose such examinations took place.
Mr Darling explained that the inquiry, headed by Michael Redfern QC, will seek to establish whether the next of kin were informed of the procedure and whether they consented to it.
British Nuclear Fuels (BNFL), the company which owns Sellafield, has confirmed that it began sampling autopsy material in the 1960s with the "historic" practice ending in the 1990s.
A Department of Trade and Industry (DTI) spokesperson said before Mr Darling's statement that "the prime concern is the feelings of the families".
His sentiments echoed those of GMB national officer Gary Smith who described the "anguish" faced by the families of those who died.
Mr Smith welcomed the inquiry announced by Mr Darling. He said: "The joint trade unions have asked for transparency and the government has committed itself to that."
Click here to run an energy price comparison, and see if you could be paying less for your gas and electricity.