"The track is fine," said Mercedes driver Hamilton who is 19 points behind team mate Nico Rosberg with one race remaining after Brazil.
"It's not even that wet now," he told his team after red flags were waved on lap 28 for the second time.
"I don't know why we're stopping. It's normal wet conditions," the race leader added as television images showed fans in the grandstands making thumbs-down gestures.
Briton Hamilton had been urging race director Charlie Whiting to bring in the safety car and let the field race but drivers had already been told much heavier rain was on the way.
The delays, with Rosberg in second place, made it unlikely the race would be completed within the time limit and opened the real prospect of half points being awarded.
Rosberg can take the title in Brazil if he wins or beats Hamilton by seven points, otherwise the battle goes down to the final race in Abu Dhabi with the German even more the championship favourite.
The race, which started behind the safety car after a 10- minute delay, was stopped for the first time after 20 of 71 scheduled laps when Ferrari's Kimi Raikkonen had a big crash on the pit straight after losing control.
The Finn, whose car spun across the track and came to rest facing oncoming traffic in the spray, was fortunate to avoid a more serious accident.
The opening seven laps were behind the safety car and Sweden's Marcus Ericsson brought it back out on lap 13 when he smashed his Sauber backwards into the barriers, coming to rest at the pit lane entry.
Racing resumed at the end of lap 19 but Raikkonen crashed seconds later.
"This is just bad, just stupid," said Ferrari team mate Sebastian Vettel who had spun off on lap 10 and ended up facing oncoming cars amid the spray.
"Red flag is what it needs, we need to stop the race. How many people do they want to crash? I nearly crashed into Kimi in the middle of the straight, I couldn't see anything," added the four-times champion.
With cars parked up, drivers waited for 35 minutes before the race could restart on extreme tyres.
After 15 minutes and seven laps behind the safety car, the action stopped again.
French driver Romain Grosjean crashed his Haas into the barriers on his way to the starting grid after losing control on standing water.
(Editing by Tony Jimenez)
