Muralitharan sat out nets on Sunday afternoon and then suffered from stomach cramps throughout the night.
After Monday morning's practice session was washed out, Muralitharan returned to his bedside for further rest.
Team sources expect Muralitharan to recover in time to take his place in the team but there are concerns about his health as Sri Lanka prepare for a crucial match.
Sri Lanka lost the opening Test in Galle by 197 runs and must win or draw in Kandy, Muralitharan's home town, to keep alive their hopes of winning the three-match series.
Sri Lanka's practice was also disrupted on Sunday afternoon and the team will return to Asgiriya International Stadium as soon as there is a break in the weather.
Thilan Samaraweera (groin) and Sanath Jayasuriya (hand) will both undergo fitness tests but Sri Lanka are increasingly optimistic about their chances of playing.