Speaking in Holyrood, Michael Matheson said Marine Scotland was tracking vessels and that new regulations in force from Tuesday would avoid a repeat of the situation in Orkney where a Russian oil tanker was blocked from docking at the Flotta oil terminal.
He also said Belarus should receive the same level of sanctions as Russia should it be verified that troops from the country are engaged in the invasion of Ukraine.
Asked what discussions the Scottish Government had had with the UK Government about the NS Champion tanker and preventing a similar issue, Mr Matheson said new regulations were set to come into force at 3pm today.
The transport secretary said these regulations prohibited the entry of vessels connected to Russia to UK ports, the registration of such vessels in the UK, and allowed the detention of such vessels in special circumstances.
He said the Scottish Government would work closely with the UK Government to “maximise effectiveness of this regime”.
Mr Matheson said there were “challenges” in the shipping sector, with vessels operating under a “flag of convenience” and many having “complex ownership structures”, making it “challenging to identify connection to Russia”.
He continued: "Marine Scotland officials are actively tracking and monitoring all Russian vessels, which are exercising the right of innocent passage in Scottish waters under international law at the present moment.
"That will continue to be the case as we go forward in the days and weeks ahead.”
The transport secretary also provided Holyrood with an explanation as to why a Russian charter flight was allowed to depart from an airport owned by Highlands and Islands Airports Ltd, blaming the issue on a delay to information being passed to airport operators.
He said “proper procedures” were followed, but there was still a “lack of clarity” around the sanctions regime which the Scottish Government will “continue to pursue" with the UK Government.
Mr Matheson also reiterated calls for Belarus to be sanctioned if reports of Belarussian troops joining the invasion of Ukraine are true.
He said: “[If correct], it would follow logic that Belarus should be subject to the same severe sanctions as Russia”.