Former Family First senator Bob Day was not validly elected at last year's federal poll, the High Court has found.

In order to determine his replacement, a special recount of Senate ballots in South Australia will be held.

According to ABC election analyst Antony Green, the seat will likely go to Family First's second-spot candidate in South Australia, Lucy Gichuhi.

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The party's South Australian chairman, Dennis Hood, said while he was disappointed by the court's decision, Family First was ready for Kenyan-born Ms Gichuhi to replace him.

"We have a quiet level of confidence, but we also want to respect that there is a court process in play and you know we will respect the decision of the court, whatever that may be in the end," he said.

The court was asked to decide whether the leasing arrangements for his South Australian electorate office had breached Section 44 of the Constitution.

The court found he had not been eligible to sit in the Senate since at least February 2016, before the July poll, because the arrangements breached the Constitution.

The law stipulates that all candidates for Parliament must not have a direct or indirect financial interest in any agreement with the Commonwealth.

However the Commonwealth leased the office space at a building owned by Mr Day in order to house his electorate office.

Mr Day later transferred the property to a family friend, but documents before the court show there was an agreement that proceeds from the rent would go to a company owned by Mr Day.

Mr Day resigned from the Senate last year after his construction business went into liquidation, but the process of replacing him has been delayed by the High Court proceedings.

A replacement could not be selected until it was determined whether Mr Day was a valid candidate when he stood at the 2016 poll.

If Mr Day had not been found to have breached the Constitution, Family First would have had a choice over who replaced him.

However, the court instead ordered a special recount of South Australian ballot papers in order to determine his replacement.

Since his resignation, Mr Day's Senate seat has sat empty, and the Government has been forced to make do without his usually supportive vote.

Attorney-General George Brandis and Minister Assisting the Prime Minister for Cabinet Scott Ryan said in a joint statement the decision confirmed the Government took the appropriate action to ask the Senate to refer the matter to the High Court.

They said the new senator would be sworn in on May 9, when the Senate meets next.