"Please know New Zealand is committed to continuing to support you," Ardern said.
Shmyhal said he was "deeply grateful" to New Zealand for its support and hoped to meet Ardern again in a "peaceful, liberated" Ukraine.
The meeting, which was kept deeply secret out of security concerns, occurred at an ominous time in the war.
Putin had recently escalated tensions in Ukraine by calling 300,000 reservists in what the Russian leader called a "partial mobilisation" and making veiled threats of nuclear warfare.
Tensions are also escalating over referendums to be held in parts of Ukraine over whether they should unify with Russia. It is believed these referendums will provide a pretext for further escalation of the war.
Ahead of the meeting, Ardern said he would be seeking Shmyhal's views "on the recent rhetoric from President Putin both around the use of potentially wider weapons of warfare", as well as "statements [Putin]'s made around referendums".
Earlier in the day, Ardern hit out at the referendums to be held by Russian-backed separatists. The polls are widely seen as an attempt to create a pretext for a broader invasion.
Ardern decried these "sham" referendums, which appear to be designed to give Putin an excuse to annex parts of Ukraine into Russia.
Putin also made a veiled threat to use nuclear or other powerful weapons if he felt it necessary.
Ardern said she spoke with Shmyhal about "the ongoing escalation we see in Ukraine".
She also reaffirmed New Zealand's ongoing support for Ukraine.
Ardern said everything she had heard from Ukraine was that New Zealand was doing a "significant amount" to assist with its efforts.
"New Zealand has always stood firmly against this illegal invasion, but we stand firmly against an escalation of this conflict."
She said the threat of escalation "flies in the face of the lie they have told that are there to liberate others".
United States President Joe Biden delivered his address to the United Nations General Assembly this morning.
In his speech, he decried Russia's escalation of the conflict and veiled threat to use nuclear weapons.
Biden said that Putin made "irresponsible nuclear threats" and repeated a longstanding American position that a "nuclear war can not be won, and must never be fought".
Ardern said the speech reflected "the time we are in".
"Even in the last 24 hours we have seen an extraordinary escalation coming from Putin."
Ardern will make her own speech to the General Assembly later this week. Earlier, she conceded that Ukraine would dominate this week at the United Nations.
Ardern and Shymhal also discussed post-conflict reconstruction and the legal institutions that could be used to hold Russia to account for its actions in the war.