Yameen's security has been tightened in the wake of the September 28 blast that wounded his wife and two others, with a special security unit having been established to protect the president, Minister at the President's Office Mohamed Shareef told AFP.
"We are now being told that it is likely to have been an attempt on the president's life," Shareef said by telephone.
He said the two people taken in Tuesday had access to the vessel "in the line of their duty", but did not say if they had any direct role in the attempted killing.
The minister's remarks mark a shift in the government account of the blast, from originally blaming mechanical failure to a suspected attempt on Yameen's life.
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Shareef's comments came days after the United Nations ruled that Nasheed's jailing was illegal and demanded his immediate release along with compensation.
Shortly after the explosion, the Maldivian government sought help from the United States, Saudi Arabia, Australia, India and Sri Lanka to carry out an investigation.
He noted, however, that new security measures were being taken to protect the president and other key dignitaries, including with the creation of a new presidential security division.