But he nevertheless dismissed as "absurd" any suggestion Ukraine had supplied the communist state with such equipment.
A report by the International Institute for Strategic Studies (IISS) said missiles used in recent North Korean tests were based on the Soviet-era RD-250 engine built at Dnipro, Ukraine.
While the IISS report did not accuse the Ukrainian authorities or the plant managers of being involved, it did suggest the engines could have been stolen from storage there.
But Kiev reacted angrily to an article in the New York Times that emphasised the engine's Ukrainian origin, in a statement posted on the president's website.
Poroshenko ordered immediate checks on the New York Times' allegations of deliveries of missile engines or related technology from Ukraine to North Korea -- and a report back in three days.
"However absurd the accusations against Ukraine are, we must carefully check... the alleged deliveries," the statement quoted Poroshenko as saying.
The high-profile probe would be overseen by Ukraine's national security council chief, Yuzhmash, Ukraine's aerospace firm and other officials.
"I am certain that this will confirm the artificiality of the claims of a 'Ukrainian trace' in the North Korean missile," Poroshenko added.
In a post on his Facebook page, he said he had given orders for New York Times journalists to be invited Ukraine to "meet Ukrainian partners who were unfairly targeted by baseless suspicions".
Earlier this week Kiev denounced the report as an "anti-Ukrainian campaign... provoked by Russian special services to cover their participation in North Korean nuclear and missile programmes".
The controversy led IISS missile expert Michael Elleman, who wrote the report that sparked the row, to clarify his position on Twitter.
"Yuzhnoye is one of several possible sources, there are other potentials in Russia" he wrote, and the current Ukrainian leadership was likely not involved or aware of any transfer.
North Korea carried out a pair of successful intercontinental ballistic missile tests in July following long-term struggles, which the IISS report said could be caused by the RD-250 purchase and refurbishment.
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