Pekka Haavisto made the comments after Turkey's President Recep Tayyip Erdogan said the country would not support Sweden's bid after a Quran was burnt outside its Stockholm embassy.
“We have to assess the situation, whether something has happened that in the longer term would prevent Sweden from going ahead,” Mr Haavisto said.
It was “too early to take a position on that now” and a joint entry into Nato remains the “first option”, he said.
The Foreign Minister said a break of a few weeks was needed in Finland and Sweden's talks with Turkey on their application to join the Nato military alliance.
"A time-out is needed before we return to the three-way talks and see where we are when the dust has settled after the current situation, so no conclusions should be drawn yet," Mr Haavisto said.
"I think there will be a break for a couple of weeks."
Outrage at Quran burning
Turkey expressed outrage after far-right figure Rasmus Paludan burnt a copy of the Quran outside its embassy in Stockholm at the weekend, an act that was strongly condemned by the UAE.
“Those who allow such blasphemy in front of our embassy can no longer expect our support for their Nato membership,” Mr Erdogan said.
The incident sparked counter-demonstrations around the world, including in Turkey, Iraq and Jordan. The Swedish government condemned the stunt but said it was a legal act of free expression.
About 200 people attended a protest on Monday night near the Swedish embassy in Amman, Jordan.
Some shouted slogans praising the Quran and condemning its “enemies”.
“Our Quran is our constitution,” some shouted. “When they burn it they burn our organs.”
The protesters gathered at a car park near the embassy as a large number of security personnel surrounded the compound.
Mr Haavisto said the protest in Sweden where the Wuran was burnt was “clearly intended to provoke Turkey”. He said he did not expect progress until Turkish elections in May.
“We are on a very dangerous path because the protests are clearly delaying Turkey's willingness and ability to get this matter through parliament,” he said.
Protests against Quran-burning in Sweden - in pictures
Even before the Quran-burning incident, Turkey had said both publicly and privately that it was particularly concerned with Sweden.
However, Finnish Prime Minister Sanna Marin said as recently as last week that the two countries should join simultaneously.
All 30 Nato allies must ratify their applications before they can join. All but Turkey and Hungary have done so. Hungary says it supports them but has not yet held a vote in parliament.
Turkey has held up the process due to concerns over how Sweden and Finland treat Kurdish groups and people Ankara considers terrorists.
Turkey has said Sweden must take a clearer stance against what Ankara sees as terrorists: mainly Kurdish militants, and a group it blames for a 2016 coup attempt in Turkey.
Initially hoping for swift approval last year, Mr Haavisto believes Ankara is unlikely to decide on whether to accept the Finnish and Swedish applications until after the Turkish elections due in mid-May.
On Monday Mr Erdogan announced that presidential and parliamentary elections would be brought forward by a month to May 14.
Mr Haavisto said he had spoken on Monday to Turkish Foreign Minister Mevlut Cavusoglu.
"Of course they feel the pressure from the upcoming elections in mid-May and because of that the discussion understandably has become heated in many ways in Turkey," he said.
Finland and Sweden have said they plan to join the alliance simultaneously and Mr Haavisto told Reuters he saw no reason to consider whether Finland might go ahead alone.
"We are in agreement that both countries' processes will continue as planned," Swedish Foreign Minister Tobias Billstrom said after speaking to Mr Haavisto on Tuesday.