Computers and papers were seized in what appeared to be an attempt to discover the identity of the person who provided information used in his Dirty Politics book.
The book was an election bombshell based on hacked email and social media material belonging to Whale Oil blogger Cameron Slater.
The person contacted the Herald and Fairfax using the identity Rawshark while using the Twitter handle @whaledump to release information publicly.
Hager said five officers came to his Wellington home last Thursday with a search warrant.
He was in Auckland at the time, giving lectures at the University of Auckland.
"Soon after the police arrived, the lead detective stated that I was not a suspect in their case, merely a witness."
Hager's sister Mandy Hager was present at the raid, and described on Twitter last night what took place.
"I observed police as they searched - polite and respectful (and slightly sheepish) - clearly strings pulled from above #dirtypolitics," she wrote.
A police spokesman told the Herald officers had not deliberately waited until after the September 20 election to conduct the search.
"No. This is a purely operational decision based on where our inquiries have led us to date."
In a media statement, a spokesman confirmed police had removed "computers and related items under search warrant from a Wellington address" as part of their ongoing investigation into alleged hacking of Slater's emails.
Hager said he told the detective there was nothing in his house that would uncover the source.
"Nonetheless, he and his four colleagues seized a large collection of papers and electronic equipment belonging to my family, including computers, drives, phones, CDs, an iPod and a camera."
Hager said the search and seizure of the material was a "fishing expedition".
"I am confident that the police took nothing that will help them with their investigation."
Hager said he would not co-operate with the police in any way to reveal the Dirty Politics source - or any other source.
"I believe the police actions are dangerous for journalism in New Zealand.
"It matters to all people working in the media who could similarly have their property searched and seized to look for sources. People are less likely to help the media if the police act in this way.
"The police want people to respect their role in society; they should in turn respect other people's roles in society."
He said he was speaking to his lawyers about challenging the police action.
University of Canterbury media law professor Ursula Cheer said Hager had legal grounds to oppose the warrant or the way it was carried out.
"I think some of his objections could be justified," she said. "I am surprised it took 10 hours and it sounds odd that it needed to be done when he wasn't there."
In a blog post last night, Slater said Hager was the recipient of stolen information and it would be difficult for him to claim journalistic endeavours.
"Journalists call people they write stories about. Journalists give people a right of reply. Journalists tell the whole story, not massaged narratives that suit their politics.
"If my emails were in the public interest to publish then his sources are public interest too. It must cut both ways."
Police said anyone with information related to the investigation could contact them, or phone Crimestoppers anonymously on 0800-555-111.
- By David Fisher and Morgan Tait of the New Zealand Herald
