Greenpeace said in allowing the ship to dock, Japan's port authority had ordered it not to open the ship to the public.
"Fundamentally, the central government didn't do anything to get in our way, but they also don't really want people to know the 'inconvenient truths' about whaling," Jun Hoshikawa, head of Greenpeace Japan, told Reuters.
Greenpeace has said the All Japan Seamen's Union pressured the ship's agent to withdraw services because it believed the group was violent, preventing it from docking last week in Tokyo.
The group called the move a violation of free speech.
Greenpeace officials said they were pleased that the ship could finally come into port but that it was unfortunate they were unable to meet with ordinary Japanese citizens.
Japan is pressing for a return to
managed commercial whaling [ICR]
The Esperanza will leave port late on Saturday.
In February, Japan abandoned its Antarctic whale hunt after fire crippled its main whaling vessel, the 8,000-tonne Nisshin Maru, and killed one crew member.
Greenpeace had offered to use the Esperanza to tow the ship, but Japan declined.
This year's hunt was also marked by clashes with anti-whaling groups, mainly the Sea Shepherd Conservation Society, one of whose boats was damaged in an incident with a Japanese vessel.
Last week, the head of Japan's whale hunt called for legal action against anti-whaling activists including Greenpeace, although both the government and the institute sponsoring the whaling programme said they were not considering such a move.
Despite an international ban on commercial whaling, Japan continues to hunt whales for what it says are scientific purposes.
It says the sale of whale meat for consumption to Japanese consumers funds research into understanding whale behaviour.
Japan is pushing for a return to managed commercial whaling saying many whale species are now at sustainable levels.