A Jakarta court on Monday ruled that Supratman was guilty of "publicly insulting" Megawati Sukarnoputri in several front page headlines in the popular Rakyat Merdeka (Free People) daily. He was given a six-month suspended prison term.
The Committee to Protect Journalists, in a statement, said it "is appalled that Indonesia is using arcane colonial laws to criminalise journalists".
"President Megawati Sukarnoputri must take immediate steps to remove defamation laws from Indonesia's Criminal Code," the New York-based committee said.
Prosecutors cited headlines from several editions: "Mega's Mouth Reeks of Diesel Oil" for a story on a decision to scrap fuel subsidies; "Mega is a Loan Shark" for a report on high bank interest rates; and "Mega is crueller than Sumanto."
Sumanto was jailed for five years in June for eating parts of a corpse.
Megawati was described as crueller than a man who was jailed for five years in June for eating parts of a corpse
Supratman argued that the headlines were direct quotes from participants in protests against Megawati.
In September the same court imposed a suspended jail term on another editor of the same newspaper for insulting parliamentary speaker Akbar Tanjung in a cartoon.
Indonesia's media was tightly controlled during the 32-year autocratic rule of Suharto, which ended in 1998.
A vigorous press has emerged since then. But media watchdog groups criticise an increasing number of law cases by public officials and others for alleged defamation.