A Labor staffer has been expelled from the party after stacking branches in federal seats, including that held by Opposition Leader Bill Shorten.

Acting Victorian Labor state secretary Kosmos Samaras has confirmed to the ABC that Haykel Handal — a former staffer for federal Labor frontbenchers Stephen Conroy and Richard Marles — was forced out of the ALP after an internal investigation into the membership irregularities.

It is alleged that Mr Handal was responsible for signing and re-signing Labor members in the federal seats of Gellibrand, Lalor, Melbourne and Maribyrnong, the latter seat held by Mr Shorten.

The ABC does not suggest that Mr Shorten was aware of the alleged branch stacking.

A spokesman for Mr Shorten said: "There is no place whatsoever in the Labor Party for this type of wrongdoing. The action taken by the Victorian branch is welcome and should serve as a warning to those who try to engage in this kind of behaviour."

The internal investigation found that in May and June last year, a "significant number" of members were signed up using a small number of debit cards, which can be bought anonymously.

It was further discovered that the cards were linked by IP addresses to one or two computers.

Although the investigation did not identify the person responsible for buying the cards and making the payments, Mr Handal was subsequently expelled from the party after a ruling by the disputes tribunal.

"I can confirm that Haykel Handal has been expelled. This decision is a direct result of an investigation instigated by the Victorian branch of the ALP. That investigation had run its course and its findings became the basis of the dispute," Mr Samaras said.

"It's important to state that we have changed our payment method protocols to ensure anonymous debit cards are no longer accepted by our system."

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However, Mr Samaras did not answer questions about whether the party would investigate whether the same method was used to sign up other members before the alleged branch stacking was discovered.

Mr Handal declined to comment when contacted by the ABC.

The ABC revealed last month that the office of a former Victorian senator was used by a Labor councillor linked to an alleged mafia boss to improperly sign up members.

Michael Teti, who has been linked to alleged organised crime figure Frank Madafferi, used the Coburg office of then-senator Mehmet Tillem in November 2013 to sign up the members.

When some of those members were contacted by the ABC, they said they had no knowledge of their membership, and had never attended the meeting.

The ABC does not suggest Mr Tillem was aware of Mr Teti's activities.