Jobs, who died last year after making his name and fortune at Apple, never got to use the yacht - called Venus - but had commissioned the French designer to work on the vessel, which cost more than€ 100m to build.
A lawyer representing Starck's company Ubik said his client had received €6m out of a €9m commission for his work on the minimalist vessel and was now seeking to recover the rest of what he was owed.
The yacht was impounded on Wednesday evening, the lawyer said, and will remain in Amsterdam port pending payment by lawyers representing Jobs' estate.
"The project has been going since 2007 and there had been a lot of detailed talk between Jobs and Starck," said Roelant Klaassen, a lawyer representing Ubik.
"These guys trusted each other, so there wasn't a very detailed contract," he said.
The lawyer representing Jobs' estate could not immediately be reached for comment.