Officials warned Justice Minister Kris Faafoi that changes to New Zealand's counter-terrorism legislation could lead to surveillance measures that disproportionally target "particular groups".
There were also concerns that putting people convicted of terror offence in jail with other serious offenders could "cement and provide an avenue for them to disseminate terrorist views".
But widening the scope of the counter-terrorism legislation was also likely to disrupt a "pattern of behaviour before it escalates to a more serious crime".
This is according to the Ministry of Justice's Regulatory Impact Statement (RIS) on the new anti-terrorism legislation.
But a spokesman for Faafoi said police must always assess whether there is sufficient time to obtain a warrant before exercising any such power.
"If there is time, they must seek a warrant from the court."
The legislation – the Counter-terrorism Legislation Bill – was introduced to Parliament this week.
Faafoi told reporters this week the proposed law would strengthen how the Government could respond to threats of terrorism.
It follows the Royal Commission into the March 15 terrorist attack, which made a series of recommendations to fill gaps in the existing law.
These include: creating a new offence to criminalise planning or preparation for a terrorist act, as well as more clearly criminalising terrorist weapons and combat training.
It also creates a new definition of a terrorist act, meaning it is one that advances "an ideological, political, or religious cause" carried out to induce "fear in a population", rather than simply "terror in a civilian population".
Faaofi told reporters he didn't think the new definition was too wide, but the justice select committee would consider whether or not this was the case.
But the RIS warned that there were some risks associated with the legislation, as it stands.
"Widening the scope of behaviours that could be captured by offences under the TSA [Terrorism Suppression Act] also creates a risk that particular groups are disproportionately targeted or perceived to be targeted by activities such as surveillance and searches used in enforcing those offences."
The RIS did not, however, say which groups this was in reference to.
But officials did say the new legislation would help to "enhance public safety".
"This will be achieved by equipping relevant agencies, such as New Zealand Police, with the appropriate tools needed to intervene early to prevent or reduce terrorism-related harm."