Police arrested 12 people yesterday after pro-Tibetan demonstrators scuffled with crowds who had turned out to welcome Xi on the first visit by a Chinese head of state to the Czech Republic.
Chinese flags hung on Prague's streets were defaced, and protesters displayed a huge billboard of the Dalai Lama with the late Czech president Vaclav Havel along the road from the airport.
Another rally against Beijing's policy on Tibet is scheduled for today outside the Czech presidential seat, the Prague Castle.
He hosted Xi at his official residence yesterday, when the two planted a ginkgo biloba tree, holding watering cans with their national flags, Czech and Chinese media reported.
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Zeman has hailed the visit as a watershed in Prague's relations with Beijing, forecasting that China could invest up to 45 billion koruna (USD 1.86 billion).
Chinese group CEFC has recently spent about 20 billion koruna in the country, buying stakes in a charter airline, a brewery, two media groups and a top football team.
"Right now we are once again an independent country and we formulate our foreign policy based on our own interests. We do not meddle in the interests of any other country."
Zeman, a 71-year-old pro-Russian leftwinger, was the only European head of state to attend a military parade in Beijing commemorating Japan's surrender at the end of World War II.
His pro-China remarks have drawn criticism from the opposition, with former finance minister Miroslav Kalousek accusing the president of "bootlicking authoritarian and unfree regimes".
The Nobel Peace Prize winner has won a global following through his spiritual teachings, but China has tried to ostracise anyone who deals with the monk.
After visiting Prague, Xi will travel to the US to attend a nuclear security summit which begins on Thursday.