Panic gripped the tiny capital as police cordoned off narrow streets and troops stepped up their presence amid heightened tensions following a blast aboard the president's speed boat in September.
But the Maldivian foreign ministry tried to defuse tension in Male by saying on Twitter: "State of Emergency NOT declared in Maldives."
The Maldivian National defence Force (MNDF) said it disabled the improvised explosive device planted near the presidential palace after evacuating residents and bystanders.
No one has claimed responsibility for planting the bomb and so far no one has been arrested, the spokesman said, though an investigation has been launched.
The discovery came a day after the US Federal Bureau of Investigations (FBI) discounted Maldivian claims of an attempt to assassinate President Abdulla Yameen by setting off an IED aboard his speed boat in September.
Yameen was unharmed, but his wife and two others were slightly wounded.
The atoll nation of 1,192 coral islands has a population of just 340,000, but welcomes more than a million foreign tourists annually.
The Maldives' image as a peaceful luxury holiday destination has, however, been dented by political unrest in recent years.
Yameen faces tough international criticism over the jailing in March of its first democratically elected leader Mohamed Nasheed, after a rushed trial which the UN said was seriously flawed.
Yameen, who came to power in November 2013 following a controversial election, faces international censure over his crackdown on supporters of opposition leader Nasheed and other opponents of his regime.
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