"We need to have the agility and flexibility to respond in an autonomous way when countries do things that are wrong," she said, adding the multilateral process - using institutions like the UN - could be "very, very hard".
Clarke said an autonomous sanctions regime was an "incredibly important" tool to "pressure countries that are not abiding by what we see as the global rules".
The Green Party has argued that an autonomous sanctions regime risked undermining institutions like the United Nations.
Clarke said this was not necessarily the case.
"If you look at what New Zealand does on the trade policy side with its approach of concerted, open plurilateralism, what New Zealand does on trade initiatives is it goes its own way. That is not undermining the global system, it is just saying 'let's make progress where we can'", Clarke said.
"At the multilateral phase it's much, much more difficult to get things done, so you do also need to have the tools to operate as an independent foreign policy actor.
"New Zealand speaks a lot of its independent foreign policy - we all do, we all have an independent foreign policy - so it's about you having your independent tools in your toolbox, but also making progress where you can and not letting the best be the enemy of the good," she said.
She said that economic pressure was the thing most likely to change Russian President Vladimir Putin's calculation on whether to push forward with the invasion.
Clarke said New Zealand and its Pacific neighbours had an interest in sanctioning Russia for its invasion.
She said New Zealand could mobilise its "international networks" to "maintain that international condemnation on Russia and make Russia feel really, really isolated, which it is".
Clark said the invasion was "not just a matter of European security, but a matter of global security.
"Russia is undermining the rules-based system on which we all depend," Clarke said.
She said New Zealand's relationships in the Pacific Islands Forum of ASEAN, could be mobilised to condemn Russia.
"New Zealand has got connections around the word. It's got great soft power as well and I think it's really important that we have a whole range of countries speaking out and condemning [Russia], not just the usual suspects that Russia will try to dismiss - the US, UK, EU," Clarke said.
"In this part of the world you've got so many small countries which have no way of defending themselves - small countries which have an equal vote in the UN General Assembly with Russia or whichever major country - we've got that system of equality in international law, one country one vote.
"But essentially what this threatens to do - what Russian aggression threatens to do - is undermine that system of sovereign territorial integrity and it threatens to bring in a regime of might is right," she said.
The Government has said that the current suite of measures unveiled against Russia would be supplemented in the coming days.
Instead of an autonomous sanctions regime, Prime Minister Jacinda Ardern appears to be leaning towards a bespoke piece of legislation designed to specifically sanction Russia.
Ardern revealed in Question Time today that the Government has sought advice on a specific "Russian Sanctions Bill", which would "target Russian finances" following a question from Act's Brooke van Velden.
Earlier in the day, Ardern alluded to what this bill might look like.
"I have been working alongside officials and colleagues about what further steps we can take," Ardern said.
Ardern said there was "potential" for "a targeted legislative response that will give us a wider range of powers that will apply sanctions to Russia fit for purpose for this situation and we expect to be able to progress that soon".
