Since Christmastime, seven Finnish freighters have been stopped in Russian harbours to be thoroughly inspected by local officials, according to the ministry.
Finland's Minister of Transport and Communications Anne Berner told news agency STT that an increase in harbour checks is causing delays and hurting the shipping firms' bottom lines.
Berner said that the ministry would be contacting Russian officials about the matter soon.
She said arrangements were being made to organise a conference call between the ministry's permanent secretary Harri Pursiainen and Russian vice communication minister Sergei Aristov to discuss the issue.
Unsuccessful attempts by Finnish traffic safety agency Trafi have reportedly already been made to contact Russian authorities to discuss the increased harbour checks.
Russia has not explained why the increased checks are being carried out.
Before the increase, Finnish freighter vessels that traverse international waters and harbours are usually only checked by officials a couple times per year.
Berner told STT that she does not think that the increased inspections were due to Finnish officials halting a Russian ship because of an oil spill last November.