The families prevented the pair from leaving the area where families have been waiting for word of their loved ones for more than a week.
It was the latest expression of fury and desperation in a disaster filled with signs that the government did too little to protect passengers. An opposition politician said he has a document showing that the ferry was carrying far more cargo than it should have been.
Relatives of the missing passengers surrounded oceans and fisheries Minister Lee Ju-young, regional coast guard chief Kim Seok-kyun and deputy chief Choi Sang-hwan.
Some of the family members shouted at the officials, accusing them of lying about the operation, demanding that the search continue through the night and asking why hundreds of civilian divers have not been allowed to join coast guard and navy personnel in searching for bodies.
About 700 divers are working at the site of the April 16 wreck, said a spokesman for the government-wide emergency task force.
Eleven crew, including the captain, have been arrested on suspicion of negligence and abandoning people in need as the ferry sank on its way from Incheon port. Arrest warrants have been issued against four of the crew. The cause of the disaster is not yet known.