Speaking on Tuesday (13 November) after meeting with Czech Prime Minister Jan Fischer, Barroso warned that the 27-country EU would be blocked if the Czech Republic sunk the treaty, which is meant to streamline decision-making and boost the bloc's global role.
"It is not in the interest of the Czech Republic to have the treaty delayed and the EU blocked," Barroso told a news conference. "I certainly hope the Czech Republic will fulfil its obligation."
The charter has been ratified by all EU nations but Czech President Václav Klaus refused to sign it, demanding guarantees the document would not pave the way for ethnic Germans expelled from his country after World War II to reclaim their property.
Fischer said his government was working on a solution that would accommodate the demands of Klaus without renegotiating the treaty and repeating its ratification.
"There are several options. We have to choose the option that would not involve re-ratification," Fischer said, reiterating that the Czech Republic should ratify the treaty this year.
One such option, Fischer said, would be for EU leaders to approve a political declaration addressing Klaus's concern at a summit late this month and commit themselves to put it as a footnote to the treaty at some point in the future.
"I am fully convinced we will succeed in completing the ratification," the pro-EU Fischer said.
Separately, the Czech Constitutional Court said it would hold a hearing on 27 October on a challenge that has been delaying ratification of the treaty.
No more Czech Commissioner?
Even if the court ruling is favourable for the treaty, the Eurosceptic Klaus wants an opt-out from the EU Charter of Fundamental Rights - part of the document - similar to that obtained by Britain and Poland in negotiations two years ago.
While Klaus would probably like an exemption to be part of the treaty, some EU governments are reluctant to grant him even a political declaration. The treaty gives the EU a long-term president and a powerful foreign policy chief.
"We should not create precedents. One should not be subject to blackmail at the last minute," one EU diplomat said.
Barroso warned that the Czech Republic might lose its representation in the executive European Commission if the country fails to ratify the treaty.
Under the EU's current Nice Treaty, the number of commissioners is set to be cut for the first time below the number of member states.
"If there is no Lisbon Treaty, there is no guarantee for the Czech Republic or any other country to have a commissioner," Barroso said.
Barroso has been re-elected to head the Commission for another five years after the term of the current EU executive expires at the end of October.
(EurActiv with Reuters.)