The Maldivian foreign ministry said police had arrested the 27-year-old man two weeks ago, on the same day President Yameen had his then vice president Ahmed Adeeb detained in connection with another alleged assassination plot in September.
"A Sri Lankan citizen is under Maldives police custody for conspiring to assassinate the Maldives president," the foreign ministry said on Twitter.
"An investigation reveals some Maldivians paid the Sri Lankan citizen to carry out the operation."
The ministry did not identify the suspect or say who was behind the alleged plot.
Sri Lanka's military said it was aware of the arrest, but asserted the man in Maldivian custody was not a member of the country's security forces.
The announcement comes a day after the government faced a barrage of criticism for using emergency powers to raid a private television station and seize its computer data.
President Yameen on Wednesday imposed a state of emergency, giving wider powers to police and armed forces to arrest and suspending freedom of assembly and movement.
Police had accused Sangu TV of uploading a YouTube video which reportedly showed three masked men issuing a death threat to the president with the flag of the Islamic State group in the background.
The Maldivian authorities had previously dismissed the video as a fake.
However, today, the foreign ministry justified the raid saying it had information that the video had been uploaded from the station, a charge the network denies.
Local media has reported that dozens of the country's citizens have travelled to Syria and Iraq to fight with Islamic State and at least five are known to have died.