Greenpeace UK director John Sauven was blocked by immigration officials on arrival at Jakarta international airport Thursday evening and was sent back that night to Britain.
"Parts of the government want to attack Greenpeace," the environmental group's Indonesia forestry campaigner Bustar Maitar told AFP. "It's obvious that some government officials are involved," he added.
In recent years, Greenpeace has run several campaigns against Indonesia-based Sinar Mas, a privately owned paper and palm oil giant which environmental groups accused of illegally logging swathes of carbon-rich and bio diverse forests.
Greenpeace campaigns have seen the likes of Unilever, Kraft, Burger King and Barbie maker Mattel cut supply chains from Sinar Mas companies, including Asia Pulp & Paper, one of the world's largest paper makers.
"Immigration never gave us any official notification that Sauven's visa had been rejected. We are still trying to find out why he was deported," Maitar said.
Immigration department spokesman Maryoto Sumadi said that Sauven had been blacklisted from Indonesia on September 29, after he was issued a business visa.
"We have good reasons for blacklisting him, but we cannot share them. It is the right of our country, just like any country, to deny entry to people in accordance with our national interests," Sumadi told AFP.
The British embassy in Jakarta said that a consular official was in contact with Sauven on his arrival at the airport.
"It is disappointing that Indonesia has taken this step. Indonesia has committed to reducing deforestation and enhancing sustainable forest management," embassy spokeswoman Putri Wulan Tary said.
Several Greenpeace activists and journalists were deported in 2009 as the environmental group campaigned on Sumatra's Kampar Peninsula, where private paper company APRIL has allegedly been destroying carbon-rich peatland.
Greenpeace's campaign ship the Rainbow Warrior was denied entry into Indonesia in 2010.
Greenpeace says its campaigns support President Susilo Bambang Yudhoyono's pledge to cut Indonesia's carbon emissions by up to 41 percent by 2020, largely through reducing deforestation.
Deforestation in Indonesia is among the fastest in the world and accounts for up to 80 percent of the country's carbon emissions, according to Indonesia's National Council on Climate Change.