U.S. plans for the radar, along with 10 interceptor missiles in Poland, are staunchly opposed by Russia, and are a subject of heated debate in both Poland and the Czech Republic.
The Czech paper cited Karel Schwarzenberg as saying in an interview with Reuters, that if the deal does not go ahead, "I would have to go to the prime minister and hand in my resignation."
Schwarzenberg said he wanted the final document, which was officially approved by the government on May 21, to be ratified by the end of 2008, but that that he was uncertain over whether this timeframe could be met.
Earlier, Czech Prime Minster Mirek Topolanek said the main document would be put forward for ratification to parliament together with a second agreement on deployment terms and conditions for U.S. service personal, which should be ready in the near future.
Once parliament has ratified the agreement, it will have to be signed by President Vaclav Klaus.
The premier said U.S. Secretary of State Condoleezza Rice is due to visit Prague to sign the missile shield agreement in early July. Schwarzenberg is expected to sign the documents on behalf of the Czech Republic.
The missile shield proposal has caused protests in the country with around two-thirds of the population against the plans, according to an April opinion poll.
There is also considerable opposition to the deployment plan in the Czech parliament, with the leading opposition force, the Social Democratic Party, demanding a public discussion on the issue.
Russia sees the proposed Central European shield as a potential threat to national security, and believes it would destroy the strategic balance of forces in Europe.