"I'm going to ask why they are now separating Sweden from Finland. These are signals we have not received before, so I'm absolutely going to raise this with (Viktor) Orban today," Kristersson told public broadcaster Sveriges Radio.
Orban and Kristersson are both attending an EU summit in Brussels on Thursday.
Helsinki and Stockholm ended decades of military non-alignment last May when they decided to join the Atlantic alliance in the wake of Russia's invasion of Ukraine.
Their applications were accepted at a June NATO summit that signalled the Western world's desire to stand up to Russia in the face of Europe's gravest conflict since World War II.
But the bids need to be ratified by all 30 of the alliance members' parliaments, which only Turkey and Hungary have yet to do.
Orban's ruling Fidesz party has said parliament will ratify Finland's bid on March 27, but "will decide on the case of Sweden later".
On Thursday, Orban's chief-of-staff Gergely Gulyas told reporters there was "a serious chance" the Swedish bid would be ratified during the ongoing parliamentary session which runs until June 15.
Turkey's President Recep Tayyip Erdogan has meanwhile also asked parliament to quickly ratify Finland's bid, but has held up Sweden's following a litany of disputes.
burs-po/jll/giv
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