Merkel met with Filat and President Nicolae Timofti in the capital Chisinau on Wednesday. Filat, 43, who heads a government of the Alliance for European Integration, was returning from the reception when the 23-year-old assailant tossed the bottle at his car.
"At the moment we do not know who the man is, nor what the motives for his action were," said Interior Ministry official Eujen Onica, adding that the man was detained on the spot. "The police are with him now."
It was the first visit by a German chancellor since Moldova gained independence from the Soviet Union in 1991. She was met by cheering crowds during the one-day visit, which German national broadcaster Deutsche Welle called “landmark”.
Merkel backs integration process
Merkel expressed support for Moldova's drive for integration with the European Union. The process toward a more solid partnership between Moldova and the EU must happen "step by step," Merkel told reporters after her meeting.
The chancellor emphasised that the first steps must involve drawing up a treaty of association and a free trade agreement. Moldova also needs to curb corruption, she added.
She also addressed Moldova's talks with Transnistria, saying Moldova needed to make "continued progress" towards mending its relationship with the separatist region.
Transnistria lies along much of Moldova's eastern border with Ukraine. The region broke away in the early 1990s, but the international community has not recognised its independence (see background).
"There is a need for Russia to withdraw its ammunition and servicemen from the left bank of the Dniester River in accordance with its international obligations. Such a move will help further promote confidence building measures and rapidly settle the conflict by peaceful methods," Timofti was quoted as saying by the Kyiv Post.
Moldova's next important meeting is due in September, when its leaders are scheduled to have direct talks with officials in Transnistria.
Moldova has shown the "most positive developments" in comparison to other countries that belong to the EU's Eastern Partnership, according to sources with the German government who spoke to the AFP news agency prior to the visit.
The EU's Eastern Partnership programme comprises Armenia, Azerbaijan, Belarus, Georgia, Moldova and Ukraine. The partnership works towards agreements that help the countries improve their ties with the EU. In return, the EU seeks to help these countries become more stable politically, economically and socially.
Ukraine is the country that has achieved the highest level of relations with the EU so far in the Eastern Partnership framework, while Belarus, which is falling prey to autocratic tendencies, is the group's laggard.