Transport Secretary Heidi Alexander will meet the chairman of National Air Traffic Services following recent air traffic control failures.
The Swindon South MP confirmed she will hold talks with Sir Warren East in the coming weeks after fresh disruption led to more than 170 flight cancellations on Monday due to a "connectivity issue" at Nats' Prestwick centre in Scotland.
This latest incident comes less than two weeks after a separate air traffic control fault on September 8 grounded more than 2,000 flights.
Ms Alexander said: "The scale of the disruption that we experienced yesterday was bad enough and to see the impact at Prestwick yesterday was obviously very concerning to me.
"For people using our airports they would feel it adds injury to insult.
"I do understand airlines feel very angry about the situation that has transpired here and I understand why passengers who have been caught up in this will feel aggrieved.
"I’ve had a full and frank conversation with the chief executive of Nats, Martin Rolfe, and expressed my anger at the situation.
"I will be looking to meet the chair of Nats in the coming weeks."
Airlines have voiced growing frustration at repeated air traffic control failures, with Ryanair renewing its call for Mr Rolfe to step down.
Speaking at a press conference in London on Wednesday, Ryanair chief executive Michael O’Leary said: "The fundamental lesson to learn about Nats is it has an incompetent, overpaid CEO who needs to be dismissed.
"Four system collapses in the last four years, at a time when no other EU ATC computer system has collapsed even once, is unacceptable.
"Sack him and put somebody efficient or somebody effective and efficient in there to run it."
Mr O’Leary estimated the September 8 incident alone cost Ryanair between €4m and €5m.
Nats has apologised for both incidents and the disruption caused.
Mr Rolfe, who became chief executive in May 2015, has overseen the company during four major outages.
These include last year's August bank holiday meltdown, which disrupted travel for more than 700,000 passengers.
A radar-related failure in July also led to the cancellation of more than 160 flights.
An initial Nats report into the September 8 issue identified a "software defect" that caused the system to fail "in the space of a millisecond."
Mr Rolfe previously issued an apology and said he took "full responsibility" for the disruption.
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