Mr Harawira applied for the recount on Tuesday because his party was concerned about the large number of discarded votes in the Maori electorate and wanted independent scrutiny of the results.
Mr Harawira also believed Maori voters had been mistreated at polling booths.
District Court Judge Tom Broadmore, who oversaw the recount, said he would direct the commission to amend the final result.
The recount had delayed the swearing in of new MPs, which was originally scheduled to take place today. The swearing in was expected to take place next week.
Mr Broadmore said in a statement that he would issue a further judgement "to record matters coming to my attention during the recount".
He said these matters were of concern to the parties, but would not affect the final result.
"Interested parties may wish to pursue those concerns though other channels."
