Aaron Gray-Block was on his way to meetings in India when immigration officials stopped him at New Delhi airport on Saturday night and put him on a flight to Kuala Lumpur without explanation, the campaign group said.
His passport was seized and only returned to him once he had landed in the Malaysian capital, the environmental group said in a statement.
"Our colleague has a valid business visa, and yet he was prevented from entering India with no reason given," Divya Raghunandan, programme director of Greenpeace India, said.
"We are forced to wonder if all international staff of Greenpeace will now be prevented from entering the country?"
Home ministry spokesperson K.S. Dhatwalia said officials were looking into the matter after seeing media reports about it.
In April the right-wing government withdrew the group's foreign funding licence, citing violations of rules by opening accounts for foreign donations without informing authorities.
A court last month ordered authorities to unfreeze some of Greenpeace's accounts, handing the group a lifeline after it faced closure of its local operations.
Greenpeace has accused the government of waging a "malicious campaign" against it. Authorities prevented one of its campaigners in January from leaving Delhi after she was placed on a suspicious persons list.
According to Indian media, a secret report by the main intelligence agency recently warned delays to key development projects being sought by Greenpeace and other activist groups could knock up to three percentage points off India's annual growth rate.
Greenpeace has been at loggerheads with the government over claims of environmental damage caused by India's heavy reliance on coal and the impact of deforestation and nuclear projects.
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