Electoral fraud charges against federal independent MP Cathy McGowan's niece and another supporter have been dropped.

Maggie McGowan, 28, and 24-year-old Sophie Fuchsen had been charged with giving false or misleading information to the Australian Electoral Commission (AEC) ahead of the last federal election.

The pair supported the north-east Victorian MP in the last federal election when she unseated Liberal Sophie Mirabella in a shock defeat.

They were studying in Melbourne at the time but changed their addresses on the electoral role to Indi before polling began.

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Prosecutors ultimately determined the two had acted within the law by voting in the electorate.

Defence lawyers told the Melbourne Magistrates Court the women had followed advice given on the commission's website.

Outside court, defence lawyer Rob Stary said the case was a terrible waste of Australian Federal Police (AFP) and prosecution resources.

"The original complainant, whoever it was that initiated it, was quite scurrilous and unfortunately we'll never discover it as a matter of privilege," he said.

"If your family lives at a particular address, and this happens in tens of thousands of cases in Australia, people go to study temporarily outside of their family home and that's what happened in this case.

"It's curious that it just happened in Indi ... fortunately, common sense has prevailed and the charges have been withdrawn."

He said if the same case occurred across Australia, courts would be "clogged with prosecutions".

Allegations 'baseless political exercise'

Ms McGowan and Ms Fuchsen did not appear in court today.

In a statement, Maggie McGowan said it was unfortunate the AEC and AFP did not recognise the allegations as a "baseless political exercise".

Cathy McGowan welcomed the decision to strike out the charges and said her supporters never had any case to answer.

"There was no conspiracy," the Indi MP said.

"As a leader in my community I will continue to stand up for young people and I am proud to be their representative in Parliament.

"They are our future and they need to be encouraged to have their say and be part of the democratic process."

The Australian Electoral Commission has been contacted for comment.