Zeman's statement Thursday countered previous claims by the Czech government rejecting Moscow's allegations that the EU and NATO member state had produced the Novichok nerve agent that was allegedly used to poison Sergei Skripal and his daughter in an English city in March.
The Kremlin said the substance had been produced by the Czech Republic, Slovakia and Sweden when denying allegations by London and its allies that Moscow was behind the March 4 incident.
"The Czech Republic produced and tested Novichok, though in a small amount, and then destroyed it," Zeman, a 73-year-old veteran leftwinger, said in a television interview on Thursday.
Zeman cited a military intelligence report but acknowledged that the country's civilian intelligence and a military history institute denied that Novichok was produced on Czech soil.
Zeman said "a paralytic poison marked A230 was tested" in the Czech Republic last November but for reasons that are unclear later cited the report as "explicitly labelling A340 as Novichok."
The foreign ministry confirmed on Friday that Czech labs had tested substances similar to Novichok through micro-synthesis, a process which it insisted is not regarded as production under international agreements.
"The paralytic poison used in the attack in Britain is marked A234 and so it's a different variety from that tested by the Czech Military Research Institute," it said, adding that the substance was immediately destroyed.
The Kremlin hailed Zeman's comments.
"The Czech Republic has acted honestly and courageously, officially recognising and revealing this information," Russian foreign ministry spokeswoman Maria Zakharova told reporters.
Dmitry Peskov, spokesman for President Vladimir Putin, said Zeman's words highlighted the "inconsistency" of the British government's claims that Russia was behind the Skripal attack.
"It's a new confirmation that the entire Skripal story is an absolute provocation," Peskov told reporters.
Josef Mlejnek, a political analyst at Charles University in Prague, said Zeman's claim reflected his staunchly pro-Russian stance.
"They (Russia) have already started using Zeman's claim in a media battle," he told AFP, going so far as to argue that "this confirms that he (Zeman) is working for the Kremlin".
According to Frantisek Bublan, who heads the senate commission in charge of defence and security, Zeman's remarks were a "pro-Kremlin act, pure and simple".
Senate president Milan Stech for his part called them "dangerous for our country".
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