The boat was spotted in November after being reported in Dutch waters and had turned off its AIS beacon, a compulsory device allowing shipping authorities to identify and track vessels.
Justice Minister Vincent Van Quickenborne, who is also Belgium's minister for the North Sea, said: "We don't know the exact motives of this Russian ship, but let's not be naive.
"Especially if it behaves suspiciously near our wind farms, undersea gas pipelines and data cables, and other critical infrastructure," he added.
Van Quickenborne said Belgian maritime authorities had begun their own investigation and were working with other North Sea coastal states to step up security.
A statement from the minister's office said: "The passage of this vessel should doubtless be seen in the broader context of the war in Ukraine."
Russia's already tense relations with the West were plunged into crisis last year when Moscow launched its invasion of Ukraine and EU and NATO members, including Belgium, responded with sanctions.
In addition to supplying Ukraine with advanced weapons, NATO powers have been looking to shore up their own defences, including against potential covert maritime sabotage.
In September last year, a series of underwater bombings destroyed sections of the Nord Stream pipelines that had previously carried Russian natural gas to Germany.
Western countries have blamed the September pipeline explosions on Russia, but Moscow has accused the West of sabotage, and neither side has produced conclusive evidence.
On January 11, NATO and the EU set up a joint working group to reinforce the protection of Europe's vital infrastructure, in particular energy supplies.
Van Quickenborne said the suspect ship had appeared to pay particular attention to Belgium's offshore wind farms.
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