EU antitrust regulators raided Brussels Airlines and TAP Portugal last week, saying the carriers may have colluded illegally to sell seats on competing routes, breaching EU rules.
The European Union executive said on Monday the raids on the offices of the airlines in Belgium and Portugal were connected to an investigation opened in February.
"The Commission has concerns that the agreements may go further than the sale of seats on routes where the two companies are expected to compete," it said in a statement.
The agreements were already a departure from the more common form of industry code-sharing, whereby an airline sells seats on a partner's flights on routes where it does not operate itself, it said.
"While the Commission was so far rather concerned about possible effects that code-share agreements may have had for consumers, it now has, in addition, reasons to suspect illegal collusion between the parties," it added.
TAP chief executive Fernando Pinto denied any collusion between the Portuguese airline and Brussels Airlines. "We are helping the investigation and the process is transparent," he told journalists.
Brussels Airlines, 45-percent owned by Germany's Lufthansa, confirmed the inspection at its premises last week. A spokesman said the carrier was co-operating fully.
The Commission is investigating similar code-sharing agreements between Lufthansa and Turkish Airlines. Companies can be fined up to 10 percent of their global turnover if found to have breached EU rules.