Prime Minister John Key said he had considered a merger when he first took office but he did not believe it was necessary.
"I just don't think we need to do that because we are merging a lot of their support services."
He also said there had already been "a massive top-down review" of the GCSB - by Cabinet Secretary Rebecca Kitteridge - and he was acting on it.
The Government Communications Security Bureau and Related Legislation Amendment Bill widens the GCSB's legal powers to spy on New Zealanders.
It gives legal authority to continue domestic surveillance work the agency has been doing with the SIS and the police under warrant for more than 10 years, according to Mr Key.
It places greater emphasis on its role of cyber security and detecting threats to government systems and private sector ones.
The work the GCSB has been doing with the SIS and police has been suspended until the law is passed.
Mr Key stepped up the political attacks on Labour for its position, suggesting that it would have to take some responsibility if an act of terrorism happened in New Zealand because spy agencies hadn't been able to continue their work.
"They might have to ask themselves if one day there was an equivalent of the Boston bombings in New Zealand, would they be the very same members who would stand up and say they prevented New Zealanders from being kept as safe as they otherwise could be."
Mr Shearer said Mr Key was trying to divert attention away from the fact that he did not have enough support to pass the bill - New Zealand First and United Future have not yet decided their positions.
New Zealand First leader Winston Peters said getting agreement to a panel to authorise warrants for domestic surveillance would be a good start.
He was concerned about protecting people's rights.
"But you are not going to see a whole lot of mangled bodies at some railway or airport in this country because we haven't done our duty."
Herald-DigiPoll
Labour and the Greens are pushing for a full inquiry into the workings of the spy agency the GCSB and the SIS. Do you agree or disagree?
• 52.1% - Agree
• 36.9% - Disagree
• 11% - Don't know
Source: Herald-DigiPoll survey of 750 people, June 12-23. Margin of error 3.6%.