President Benigno Aquino's spokesman Herminio Coloma said the nine, who were convicted on Monday for catching endangered sea turtles, merely have to pay a fine in order to walk free.
"For the offence pertaining to possession of endangered species, the court imposed a penalty of payment of fines. Upon payment of the fines, they are deemed to have served the penalty fully, and there is no further impediment for them to leave the country," he told reporters.
"We must respect the decision of the court," he said in a statement.
The nine were found guilty on Monday and fined USD 100,000 each for poaching with an additional 120,000 pesos (USD 2,730) fine for catching an endangered species.
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The case has strained relations between China and the Philippines, who are engaged in a bitter territorial dispute in the South China Sea.
Filipino police said they found hundreds of sea turtles -- a protected species -- on board the fishermen's vessel when they arrested the group in May at Half Moon Shoal, located in a part of the sea claimed by both countries.
Beijing claims almost all of the South China Sea -- which is home to crucial shipping lanes, vast fishing areas and potentially valuable mineral resources -- including areas close to the coastlines of other nations.
Its claims conflict with those of Brunei, Malaysia, Taiwan and Vietnam as well as the Philippines.
In March the Philippines filed a formal plea to the United Nations challenging China's claims in the South China Sea, but Beijing has rejected UN arbitration.