The court fined the three men convicted 10 million naira ($26 300) each for each of the two counts of piracy to which they pleaded guilty.
The remaining six pleaded not guilty and their trial continues.
Nigerian navy spokesman Commodore Suleiman Dahun said the convictions were the first conviction under the law, passed last year to make it easier to prosecute pirates.
He said the fines were levied in lieu of prison sentences.
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While the Gulf of Guinea spans more than a dozen West African countries, experts say the pirates typically come from Nigeria's oil-rich but poverty-stricken Delta region.
Previously, attackers rarely faced judicial consequences as piracy was not illegal under Nigerian law.
A total of 49 crew were kidnapped in the Gulf in the first half of this year, compared with 27 last year, according to IMB figures. It said attackers were also going further out to sea.
"We need to change the risk-to-reward ratio...," IMB Director Michael Howlett said last month. "Without an appropriate and proportionate deterrent, pirates and robbers will get more ruthless and more ambitious."
($1 = 380.5000 naira)