The families will visit 10 Pakistani jails, check prison records and meet all prisoners of Indian origin, an Indian defence ministry spokesman said.
They are to begin their two-week search in the eastern city of Lahore.
Both India and Pakistan hold scores of civilians, many of them fishermen who stray into each other's waters, as prisoners.
In recent years, they have swapped prisoners to build goodwill. One Indian government official, speaking unofficially, said there is little chance of any PoW being found in Pakistani prisons.
"If they find even one man, it will be the scoop of the century," he said.
Some of the families, though, are more hopeful.
Bharat Suri, whose brother is among the missing, said his family's visit marks a new chapter in the history of India and Pakistan.
"I am very much hopeful and grateful to President Musharraf who has given us a chance," he said.
India and Pakistan have fought three wars since Pakistan gained its independence in 1947.