Derek Mackay is meeting other finance ministers for a "quadrilateral" summit in Edinburgh.
He said he would raise "unnecessary" tax burdens with the chief secretary to the treasury during the meeting.
The Treasury said Scottish ministers had been advised of the tax situation before setting up national services.
Most other police and fire services in the UK are regional bodies and do not have to pay VAT.
The issue arose because Scotland's policing and fire services were previously controlled by local councils, which can claim back the tax - but the new national forces set up in 2013 are controlled by the Scottish government, which cannot.
Mr Mackay said the police and fire services were struggling with the "unnecessary" burden of tax which they "simple should not have to pay".
He said: "This is a significant sum which other emergency services do not have to meet.
"There is a significant difference in the way VAT affects emergency services across the UK, with Scottish police and fire services paying VAT when other territorial services in the UK do not have to.
"There needs to be a level playing field for such essential services.
"As we continue to invest in our emergency services we will continue to press the UK government for Scottish emergency services to have the same ability to recover VAT as all other British and Northern Irish Forces."
Scottish Lib Dem MSP Liam McArthur said it was right that the VAT position was "reconsidered", but said the Scottish government should not use that as a "smokescreen" for its own failures.
He said: "The financial mess that Police Scotland find itself in is down to the SNP's botched centralisation. Ministers cannot duck that."
A Treasury spokeswoman said: "In 2012 the Scottish government chose to make Scotland's police and fire services national rather than regional bodies. The Scottish government were advised in advance that by making this change Scottish police and fire services would become ineligible for VAT refunds."
First Minister Nicola Sturgeon raised the issue during a clash over police budgets with Tory leader Ruth Davidson at Holyrood in December.
Ms Sturgeon argued that the UK government had changed the rules to exempt academy schools from VAT when they were set up and funded by the central government.
She said there was "£25m a year which should be going to our police service but is going to the Treasury".
Ms Davidson replied: "The Scottish government was warned about VAT - it knew what would happen and it did not listen to parliament. You know that the first minister is in trouble when she cannot answer for herself but runs to 'Westminster bad'."
There have been a series of warnings from auditors about financial management within Scotland's police service, which faces a funding gap of up to £200m in the coming years.

The Englishman began the day leading by three but saw his advantage wiped out when he bogeyed the eighth and Nicolas Colsaerts sank his third birdie.
Fitzpatrick, 21, regained the lead with a birdie on the 10th and hit three more from the 13th to finish on 15 under.
Defending champion Alex Noren of Sweden is level with Colsaerts after a 67.
Noren had seven birdies in his five-under round, including four on the trot from the 12th.
He is still well adrift of Fitzpatrick, who parred his first seven holes before dropping just his second shot of the week on the eighth.
The Englishman, who finished seventh at the Masters, bounced back immediately with four birdies in seven holes to move back to the top of the leaderboard.
"I find the front nine more difficult than the back nine, especially in the wind but I stayed patient and got my rewards," he said.
"It's one of the things I've learned since turning pro."
Scotland's finance secretary is to call on the UK government to scrap a £35m annual tax bill for the country's police and fire services.
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Matt Fitzpatrick extended his lead to five shots at the Nordea Masters in Stockholm by shooting a four-under-par 68 in Saturday's third round.