Other users reported the videos and the Government separately raised it with the company on Friday night.
A spokesperson for the Prime Minister said Twitter's automated reporting function failed to identify the content as harmful.
Twitter advised the Government overnight on Friday the clips had been taken down and it would do a sweep for other instances.
Fifty-one people died and about 40 more were injured in two attacks on Christchurch mosques during Friday prayers on March 15 in 2019. The lone gunman had filmed the attack.
He pleaded guilty to the shootings at the Al Noor mosque and the Linwood Islamic Centre, was convicted and sentenced to life without parole.
The Prime Minister's office said as a member of the Christchurch Call community of 120 governments and online service providers, Twitter was expected to remove terrorist content published on its platform.
Netsafe's chief safety office Sean Lyons has reminded people they can face criminal charges for interacting with illegal online content.
Lyons said if people saw anything concerning, they should report it immediately to the platform concerned and to the Department of Internal Affairs.
He said the Christchurch terror footage has resurfaced before and can be swiftly dealt with.
Meanwhile, new Twitter owner Elon Musk has tweeted hate speech messages have dropped by a third in the last few days compared with a peak of more than 10 million on 20 October.
