The two men, 33-year-old Junichi Sato and 43-year-old Toru Suzuki, were arrested in 2008 for stealing a 50-pound box of whale meat they said was destined for the black market. The two were given sentences of 1 year in prison each. The sentences were suspended for 3 years.
The judge in the case said the duo, dubbed the Tokyo Two, carried out "questionable" activities when they took the meat from the Japanese whaling ship Nisshin Maru.
The duo, however, said the sentences were "unjust," London's Independent newspaper reports.
A Greenpeace spokesman said the sentencing has a "chilling effect" on the campaign against whaling in Japan.
Supporters of the environmental group protested the suspended sentences with signs that read "Activism is not a crime."
A representative from the Japanese fisheries agency said the pair "deserved their sentence" because they violated the law.