The development is expected to unblock a large financial assistance package for war-ravaged Ukraine.
Populist Slovak Prime Minister Robert Fico welcomed the development, calling it "good news".
Hungary and Slovakia were locked in a feud with Ukraine since Russian oil deliveries to Hungary and Slovakia through the pipeline were halted in January after the pipeline was damaged.
Ukrainian officials blamed the damage on Russian drone attacks.
Hungary's nationalist prime minister, Viktor Orban, who was recently defeated in an election, accused Ukraine of deliberately delaying repairs, which Ukrainian President Volodymyr Zelenskiy denied.
Fico said on Thursday he still did not believe the pipeline was damaged at all and alleged the pipeline and oil "were used in the current geopolitical battle".
Ukraine and most of its European backers oppose imports of Russian oil which have helped to fund Russian President Vladimir Putin's war against Ukraine, now in its fifth year.
But unlike the rest of the European Union, Hungary and Slovakia still depend on Russia for their energy needs.
For two months, the two countries have accused Ukraine of failing to repair the damaged pipeline.
Citing the issue, Hungary blocked a massive EU loan to Ukraine while Slovakia refused to support new sanctions against Russia until the supplies resumed.
The flow resumed after three months early on Thursday, the Slovak economy ministry said, lifting a major obstacle to approving the EU funds for Ukraine later on Thursday, just as EU leaders gather for a summit in Cyprus.
Ukraine desperately needs the 90 billion euros ($A147 billion) loan package, originally agreed in December, to prop up its war-ravaged economy and help keep Russian forces at bay for the next two years.
The 27-nation EU had originally intended to use frozen Russian assets as collateral for the loan, but that option was blocked by Belgium, where the bulk of the frozen assets are held.
In December, the Czech Republic, Hungary and Slovakia agreed not to stop their EU partners borrowing the money on international markets as long as the three countries did not have to take part in the scheme.
But Orban, who has repeatedly blocked EU aid to Ukraine, angered the other 24 countries by later reneging on that deal over the pipeline dispute and as campaigning heated up before the April 12 election that he lost in a landslide.
The EU has also been trying since February to push through new sanctions against Russia, which Hungary and Slovakia have blocked due to the oil feud.
Fico said he expected both issues to be solved on Thursday.
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