The mission will resume if weather conditions improve in the search area, it added.
Because of the rough seas, Australian navy ship HMAS Success left the search area early in the day, the AMSA said, adding that the ship will return to the search area once the weather permits.
"A sea state ranging between 7 to 8 is forecast today with waves up to two meters and an associated swell of up to four meters," it said, adding that "the area is also forecast to experience strong gale force winds of up to 80km/h, periods of heavy rain, and low cloud with a ceiling between 200 and 500 feet (60 and 150 meters)."
The AMSA said current weather conditions would make any air and sea search activities "hazardous" and "pose a risk to crew."
"Therefore, AMSA has suspended all sea and air search operations for today due to these weather conditions," it said.
The organization also said that weather conditions were expected to improve in the search area in Tuesday evening and over the next few days.
Monday night, HMAS Success failed to locate objects sighted earlier by a RAAF P3 Orion aircraft.
Late Monday, Malaysian Prime Minister Najib Razak told a press conference in Kuala Lumpur that the missing plane "ended" in the southern Indian Ocean.
The conclusion was made by the UK Air Accidents Investigation Branch and Inmarsat, the UK company that provided the satellite data, according to the Malaysian prime minister.
"This is a remote location, far from any possible landing sites," said Najib, adding that more details will be announced at a press briefing Tuesday morning.
The announcement ended more than two weeks of wild speculation over the fate of the plane and dealt a devastating blow to relatives who had been still clinging to the hope their beloved ones might somehow survived.