"I have not observed, during the last two weeks, that Portugal and Spain had a diabolical plan to cause Tsipras' government to fall," Juncker said at a news conference at an energy summit in Madrid.
"If I had the impression that they harboured such detestable plans I would have intervened," he added when asked about the simmering row between Greece and its eurozone partners Spain and Portugal.
Madrid and Lisbon lodged a formal complaint with the European Commission over the comments by Tsipras, who likened pressure from Spain and Portugal during negotiations over a four-month bailout extension to blackmail.
During a speech to the central committee of his Syriza party on Saturday, Tsipras said Greece came up against "an axis of powers led by Spain and Portugal" who tried to scupper the negotiations to "avoid internal political risks".
"Conservative forces (in Europe) tried to set a trap for us, to drive us into financial asphyxia," the 40-year-old said.
The row between the so-called Club Med countries that border the Mediterranean Sea comes as centre-right governments in Spain and Portugal face the rise of anti-austerity parties buoyed by the rise of Tsipras's hard-left Syriza party.
Portugal has just completed a painful international bailout, sticking to the harsh austerity terms rejected by Syriza while Spain had to ask Brussels for special help with its banks.
The EU said Monday it was trying to mediate in the row.