Embassy staff "were involved in organising unlawful actions" when counter-demonstrators approached the rally, said the foreign ministry.
On August 23, more than a hundred Lithuanians linked hands in the capital's central square, in solidarity with Hong Kong activists holding a similar demonstration on the same day.
The Lithuanian action referred back to the famous "Baltic Way" protest three decades ago when the country was still part of the Soviet Union -- which in turn inspired the protesters in Hong Kong.
Counter-demonstrators waving Chinese flags approached the rally in Vilnius, triggering a disturbance and police later fined two Chinese citizens for disturbing public order.
Lithuania's Foreign Minister Linas Linkevicius said Monday that some Chinese diplomats "were more active than they should be".
"Some diplomats crossed limits, (behaving in ways) that are incompatible with their diplomatic status," the minister told AFP.
"We expressed regret and urged them to make sure that similar actions are not repeated," he added.
The Chinese embassy in Vilnius was not immediately available for comment on Monday.
The August 23 demonstrations in Lithuania and Hong Kong echoed the famous 1989 pro-democracy "Baltic Way" mass protest against Soviet rule.
More than one million people linked hands -- across Lithuania, Latvia and Estonia -- to form a human chain spanning over 600 kilometres (370 miles).
All three territories, Soviet republics at the time, were protesting rule from Moscow. They won their independence two years later.