London Luton Airport Operations Limited (LLAOL) also applied to amend the day and night noise contours.
A decision has been taken on his behalf to hold a local inquiry in due course to consider "all the relevant aspects of the proposed development".
A LLAOL spokesman said today: (Thursday, April 7) “We're disappointed by the decision, but respect the Secretary of State’s request for the application to undergo further examination.
"The government understands that airports are an important enabler of wider economic growth. For London Luton Airport to play its part, it’s important we can maximise our potential.
"Our plan enables us to do that by putting the airport on the best possible footing for a long-term recovery which supports the local economy and creates jobs, after the worst crisis our industry has ever faced.
"This plan is consistent with our commitment to achieve carbon neutrality for our own operations by 2026, and to achieve net zero emissions by 2040.”
The decision revealed in a letter to the local authority's planning consultant David Gurtler coincides with the end of a consultation period over airport expansion to cater for 32m passengers a year.
Recent exhibitions were staged at a number of venues in parts of Bedfordshire, Buckinghamshire and Hertfordshire to outline future expansion proposals of the borough council's airport company, Luton Rising.
A Luton Rising spokesman said today: "The Secretary of State had signalled his wish already to consider reviewing the (LLAOL) application, so this development is in line with due process."
A date has yet to be set for the inquiry which will be arranged by the government's planning inspectorate, according to the letter, following the decision made by Minister of State for Housing Stuart Andrew on behalf of Mr Gove.
Local protest group Luton and District Association for the Control of Aircraft Noise (LADACAN) has welcomed the government's decision.
"We're really grateful for the support from local MPs, councils and other groups in helping to get this decision called in," said Andrew Lambourne, from the anti-noise organisation.
"We expect the hearings to shine some uncomfortable light on how the borough council and the airport failed to ensure the required balance between growth and mitigation, apparently focusing on maximising revenues instead."
The letter added that the local inquiry will focus on "the extent to which the development is consistent with government policies for meeting the challenge of climate change, and for conserving and improving the natural environment".
It will also consider "the extent to which it's consistent with the development plan for the area, and any other matters the inspector considers relevant".
LLAOL received permission in 2013 to expand capacity to 18m passengers a year over a 15-year period to 2028, but reached 19m by 2019.