Air travellers are facing another day of disruption at several European airports including Heathrow, after a cyber-attack knocked out a check-in and baggage system.

There were hundreds of delays on Saturday after the software used by several airlines failed, with affected airports boarding passengers using pen and paper.

Brussels Airport said it had “no indication yet” when the system would be functional again and had asked airlines to cancel half their departing flights for Monday.

RTX, which owns software provider Collins Aerospace, said it was “aware of a cyber-related disruption” to its system in “select airports” and that it hoped to resolve the issue as quickly as possible.

It identified its Muse software – which allows different airlines to use the same check-in desks and boarding gates at an airport, rather than requiring their own – as the system that had been affected.

The company has yet to disclose what went wrong or how long it expects the outage to last, but said on Sunday it will “provide details as soon as they are available”.

Brussels Airport said only manual check-in and boarding are possible “due to a cyberattack against Collins Aerospace”.

It added disruption would continue into Monday “because Collins Aerospace is not yet able to deliver a new secure version of the check-in system”.

Heathrow said on Sunday that efforts to resolve the issue were ongoing. It declined to say whether or not the issue was a cyber attack.

It apologised to those who had faced delays but stressed “the vast majority of flights have continued to operate”, urging passengers to check their flight status before travelling to the airport and arrive in good time.

The BBC understands around half airlines flying from Heathrow were back online in some form by Sunday – including British Airways which has been using a back-up system since Saturday.

There have already been more cancellations across Heathrow, Berlin and Brussels so far on Sunday than throughout Saturday, according to flight data firm Cirium, though not all of these are due to the cyber-attack.

There were hours-long queues on Saturday and some 47% of Heathrow’s departing flights were delayed, according to flight tracker FlightAware. Additional staff were at hand in check-in areas to help minimise disruption.

By Sunday afternoon, FlightAware data showed the number of delayed flights from Heathrow had fallen from levels seen on Saturday.

Virgin Atlantic, which operates from Heathrow, said it was “aware of a technical issue impacting check-in systems at a number of airports including London Heathrow which may result in some delays to departures”.

It added that “currently all Virgin Atlantic flights are scheduled to depart as planned”.

Naomi Rowan, from Sudbury in Suffolk, was supposed to be moving to Costa Rica with her dog Dusty, but both are now in a hotel after their Air France flight from Heathrow on Saturday was affected by the cyber attack.

She said staff were boarding passengers with pen and paper due to the outage but told her they were unable to board Dusty without the electronic system.

“I had a cry, booked a hotel and managed to get through to Air France on WhatsApp, who say the next available flight for me is Monday,” she said.

Europe’s combined aviation safety organisation, Eurocontrol, said airline operators had been asked to cancel half their flight schedules to and from the airport until 02:00 on Monday due to the disruption.

Meanwhile, Dublin Airport said that while the technical issues persisted and some airlines were continuing to check in manually, it was expecting to operate a full schedule on Sunday.

A spokesperson told the BBC: “Passengers are advised to contact their airline directly for updates on their flight.”

Dublin Airport previously said that Cork Airport, which is owned by the same parent company, had experienced a “minor impact” from the cyber-attack – but Cork Airport has since said it has faced no disruption with all services operating as normal.

Berlin Brandenburg Airport is asking travellers to use online or self-service check-in instead of the desks while the outage is ongoing.

It said there had been 12 cancellations in and out of the airport on Saturday, but that delays were generally less than 45 minutes.

A National Cyber Security Centre spokesperson said on Saturday that it was working with Collins Aerospace, affected UK airports, the Department for Transport and law enforcement to fully understand the impact of the incident.

The European Commission, which plays a role in managing airspace across Europe, said it was “closely monitoring the cyber-attack”, but that there was no indication it had been “widespread or severe”.

Transport Secretary Heidi Alexander also said she was aware of the incident and was “getting regular updates and monitoring the situation”.

It was only last July that a global IT crash due to a faulty software update from cybersecurity firm Crowdstrike caused disruption to aviation, grounding flights across the US.

Analysts said at the time that the incident highlighted how the industry could be vulnerable to issues with digital systems.

Additional reporting by Rozina Sini