Passengers of a cruise ship and a ferry at Station Pier in Melbourne have been given the all clear, after being evacuated as a precaution when sniffer dogs smelt "something suspicious".

Victoria Police were called to the scene at 12:15pm and the bomb squad also investigated.

The area was then deemed safe shortly after 4:00pm.

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"Bomb Response Unit has deemed the area at Station Pier safe," Victoria Police tweeted.

"Cruise ship passengers aren't yet able to board but will be advised shortly."

Earlier, police said nothing had been sighted and the evacuation was a precaution only.

The two ships at the port are the Spirit of Tasmania and the Noordam.

Passengers were left waiting on the pier.

Robert Green, a tourist from California, said he was frustrated that they were not being told what was going on.

"No-one will tell us. We have not a clue," he said.

"There's a lot of guess work but not a soul has told us why we cannot return to the ship."