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Two men were seen to jump ship into the Swale this morning and run off along railway lines at Kingsferry Bridge.
Police in two launches have been searching the area for the men who had been on a cargo boat loaded with gypsum and heading towards Ridham Dock.
Officers were also searching the banks of the Swale along the Sheppey coast.
The men are believed to be illegal immigrants. Another was said to have remained on board the ship.
The ship, the Aberdeen, later berthed at Grovehurst. It is understood it is carrying supplies for the Knauf plasterboard factory.
An eyewitness said: "Two immigrants jumped a boat, climbed up and ran along the railway tracks.
"Railway engineers were trying to sort it out but I think they couldn’t catch up to them."
She said the men ran off towards Elmley Nature Reserve.
A spokeswoman for British Transport Police said: "We assisted Kent police following reports of two trespassers on the line near Queenborough at 10.19am."
She said Kent police arrested the men and took them into custody.
Neither Kent Police nor Border Force have replied to requests for information.
Eighteen 'illegal immigrants' were found hiding in a lorry trailer on the M26 last month.