French designer Philippe Starck claims Mr Jobs' heirs still owe him 3m euros of a 9m euro fee for the project, according to Dutch paper Het Financieele Dagblad.
Mr Starck called in the debt collectors and had the yacht impounded,
The Port of Amsterdam confirmed that the boat is not allowed to leave.
Jeroen Ranzijn, spokesman for the Port of Amsterdam told the BBC: "The boat is brand new but there is a 3m euro claim on it. The parties will have to fight it out."
Roelant Klaassen, a lawyer representing Mr Starck's company, Ubik, told the Reuters news agency that the boat would remain in port pending payment by lawyers representing Mr Jobs' estate.
"These guys trusted each other, so there wasn't a very detailed contract," he said.
Mr Starck was unavailable for comment.
Gerard Moussault, the lawyer representing the owners of the Venus told the BBC: "I cannot comment at all on this, sorry."
The sleek, 260ft-long (80m) aluminium super-yacht cost 105m euros ($138m; £85m) and was launched in October, at Aalsmeer, The Netherlands.
Mr Starck collaborated with Steve Jobs for five years on the project, describing the boat as "showing the elegance of intelligence."
Mr Jobs died of pancreatic cancer in 2011 and never saw his boat go to sea.
BBC News - Steve Jobs' high-tech yacht impounded over bill dispute
word is google is willing to pick up the bill