Presidential spokesman Ibrahim Muaz Ali announced the sacking of Defence Minister Moosa Ali Jaleel in a tweet, but gave no further details. The government has not yet announced his replacement.
"The president has dismissed Defence Minister Moosa Ali Jaleel," the spokesman tweeted in the Maldivian language Dhivehi.
It followed a reshuffle of key security officials in the wake of the September 28 explosion aboard Yameen's boat, as he was about to disembark at the capital island Male.
Maldivian authorities have arrested two security personnel who had access to Yameen's boat but have yet to disclose what caused the explosion.
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Jaleel was given the job in January soon after the sacking of his predecessor Mohamed Nazim, who has since been tried and convicted of smuggling arms and jailed for 11 years.
In July, President Yameen secured parliamentary backing to impeach another former ally, his vice president Mohamed Jameel.
Nasheed, the country's first democratically elected president, was jailed for 13 years on terrorism charges in March.
A UN panel ruled last month that his incarceration was illegal and he should be freed immediately.