The anti-dumping investigation will look into charges Canada's Bombardier receives subsidies of nearly 80 per cent, and could lead the US Commerce Department to impose punitive import duties of that amount.
The preliminary ruling on the 100-150-seat planes is due by June 12.
"The US market is the most open in the world but we must take action if our rules are being broken," Commerce Secretary Wilbur Ross said in a statement.
The petition followed Washington's decision to slap tariffs on Canadian imports of softwood lumber. Since Trump took office in January, an aggressive stance on trade has set relations with America's neighbours on edge.
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Boeing complained last month that Bombardier was marketing its C Series passenger jets in the United States for less than it costs to produce them, which could undercut sales of Boeing 737 passenger jets.
The Canadian aircraft subject to the investigations have not yet been imported, but the Commerce Department cited an April 2016 statement announcing the pending sale of Bombardier aircraft to Delta Air Lines in an order valued at USD 5.6 billion.
Bombardier said last month it worked to ensure compliance with the laws of countries where it operates and spent about USD 3 billion annually with American suppliers.