Express Newspapers, publisher of the Daily Express, Sunday Express and Daily and Sunday Star, will no longer be able to use the newspaper trade body's services, which protect and promote national newspapers.
David Newell, director of the NPA, said: "The Council of the Newspaper Publishers Association agreed on Friday to terminate Express Newspapers' membership of the NPA.
"The Council has written to the publisher explaining the reasons for this decision which relates to non-payment of invoices due in 2006."
In May, Express Newspapers' owner Richard Desmond ended its investment in the Newspaper Marketing Agency.
The NPA, which was founded in 1906, monitors and lobbies activities on UK and European legislation affecting the newspaper industry. It also deals with labour relations and management services for the industry, and training and management development.
Its current members include: Associated Newspapers; Financial Times; Guardian Newspapers; Independent Newspapers (UK); MGN; Trinity Mirror's national titles; News International; and the Telegraph Group.
Express Newspapers was unavailable for comment at time of publication.
Express Newspapers, which is owned by Richard Desmond, has also been in dispute with the Telegraph Media Group over their joint printing venture at the Westferry plant.
Murdoch MacLennan, Telegraph Media Group chief executive, recently called up Desmond for scaremongering stories, claiming that the Telegraph Group was refusing to pay its half of a £66m pension deficit.