The statement yesterday came as Chinese firms poured fresh investment into the Czech Republic, for a value expected to reach a total of several billion euros.
The Czech president, prime minister and two parliamentary speakers said that the EU nation "respects the sovereignty and territorial integrity" of China.
"We consider the relationships between our countries and their remarkable development in recent years most beneficial for both parties," the statement added.
Czech President Milos Zeman, an ex-Communist in office since 2013, has promoted friendly relations with both Russia and China.
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The Dalai Lama fled to India after a failed uprising in 1959, but is still deeply revered by many Tibetans in China and beyond.
He arrived in Prague on Monday to attend the pro-democracy Forum 2000 conference, co-founded in 1996 by former Czech president Vaclav Havel.
Since Havel died in 2011, Czech foreign policy has taken a turn eastwards.
Chinese President Xi Jinping visited Prague with a business delegation in March.
China's CEFC, one of the country's top 10 private firms, recently spent around a billion euros on stakes in a Czech airline, a brewery, two media groups and a top football team.
"The private activities of some Czech politicians do not signal a change in the Czech Republic's official policy and we would consider it unfortunate if someone perceived them as such," said the leaders.
Before coming to Prague, the Tibetan spiritual leader met Slovak President Andrej Kiska in Bratislava, angering Beijing which threatened retaliation, according to local media.
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