Transdniestr, which borders Ukraine and is mainly Russian-speaking, declared independence from Moldova in 1990 and has Russian troops stationed there but is not recognised by any country.
Dmitry Rogozin, who is also President Vladimir Putin's special representative to Transdniestr, visited the separatist region for Friday celebrations marking victory over the Nazis in World War II.
Russia's annexation of Crimea has prompted fears it could claim other disputed ex-Soviet regions with majority Russian-speaking populations.
"The signatures of the Transdniestrians on recognising the republic are in Moscow. The Moldovan special services who delayed our flight just got the smaller part of our cargo," Rogozin boasted on Facebook.
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Chisinau said late yesterday that it had "seized these materials in order to examine them".
It slammed Rogozin's "unproductive" acts and "provocative statements on Moldova", saying they "do not help to make progress in the Transdniestr conflict."
"Chisinau's provocation will have serious consequences for our bilateral relations," Rogozin said.
His visit coincided with Putin's making his first trip to Crimea since annexation.
Rogozin wrote angrily on Twitter that Ukraine prevented his plane from flying over its airspace on the outward journey from Moscow, while on the return flight EU member Romania barred his plane from its airspace.
"Next time I will fly in a Tu-160" strategic bomber, he wrote.