The statement came just over a week after the Czech government said it suspected that two Russian agents were behind the deadly explosion at an ammunition factory.
Czech President Milos Zeman has cast doubt on Russia's involvement in a 2014 explosion at an arms depot.
President Zeman has suggested the deadly blast could have been caused accidentally due to the mishandling of explosives and says there is no conclusive evidence to charge Russia over the alleged sabotage.
Prague caused an unprecedented diplomatic crisis by accusing two Russian GRU intelligence agents of involvement in the blast in Vrbetice, which killed two people.
Czech prime minister Andrej Babis had said that there was "irrefutable evidence" to charge the Russian nationals, following investigations by the Czech counterintelligence service.
But the pro-Russian President contradicted his government's stance in a televised address on Sunday.
"We are working with two versions of the investigation; the first is that the explosion occurred after manipulation by unspecialised personnel," Zeman said.
"And the second, that there was foreign espionage intervention. I seriously consider both versions possible," he added.
The head of state also warned against "any form of hysteria" and called on the Czech Republic to wait for the results of an official probe.
An investigation into the explosion has now been taken over by the Czech state prosecutor.
The Czech coalition government named two Russian suspects linked to the 2018 Salisbury nerve agent poisoning in the UK and initially expelled 18 Russian embassy staff.
Moscow has fiercely denied the allegations and expelled a number of Czech diplomats in retaliation. This prompted Prague to order a further 63 diplomats and Russian staff to leave the country by the end of May.
Slovakia, Estonia, Latvia and Lithuania have also expelled Russian diplomats as a sign of solidarity with the Czech Republic. The EU and NATO also issued statements in support of the Babis' government.
On Monday, the Romanian Foreign Ministry also said it had declared a diplomat in their Russian embassy a "persona non grata".
Romania's Russian ambassador Valeri Kuzmin was summoned and informed of the decision, the ministry said in a statement.
After his televised address, opposition politicians in the Czech Republic have accused the president of spreading disinformation.
"It was not a speech for Czech citizens, but for the Russian Federation," tweeted Markéta Pekarová Adamová, leader of TOP 09.
"Trivialisation, raising doubts, slandering, It's all cleverly wrapped," she added.
Pavel Fischer, chairman of the Czech senate committee on foreign affairs, defence and security, said that Zeman's doubts had damaged the country's reputation.
"With his manipulative statements, Zeman directly undermines the defence of his own state," Fischer said in a Facebook post.
"Zeman already stands on Russia's side and became his advocate."