North Macedonia's foreign ministry also strongly condemned the incident and said they would investigate to find the person responsible.
Bulgaria has summoned a North Macedonian official after a flag was vandalised near their embassy in Bitola.
The Bulgarian foreign ministry said that the pylon next to their embassy in North Macedonia had been damaged over the weekend. The country's national flag had also been removed, they said.
The ministry described the incident as "yet another act of desecration of Bulgarian national symbols in the Republic of North Macedonia."
Bulgarian officials have raised concerns over "increasing cases of attacks and acts of aggression provoked by hatred towards Bulgaria."
Sofia said they had summoned the interim head of the North Macedonian embassy and handed him a protest note following the vandalism.
"Deep indignation was expressed at this incident," the foreign ministry added in a statement on Tuesday.
"Any action expressing hatred against another country or its citizens contradicts the fundamental values of modern democratic societies and hinders the promotion of good neighbourly relations."
Meanwhile, the North Macedonia foreign ministry also strongly condemned the incident and said they would investigate to find the person responsible.
"This vandalism and irresponsible act ... should in no way be equated with the population of this traditionally consular and cosmopolitan city," a statement read.
"Such isolated and uncontrolled behaviour does not contribute to the efforts to deepen friendship, good neighbourliness, and cooperation between the two countries," the ministry added.
North Macedonia also stated that the incident harms efforts to further integrate Skopje with the European Union.