MPs have supported a motion which aims to force the Government to publish communications connected to prorogation and documents linked to no-deal Brexit planning by 311 votes to 302, majority nine.
Mr Gove called attempts by MPs to compel the Government to publish documents relating to Operation Yellowhammer and communications relating to prorogation a fishing expedition.
He said: "This is a fishing expedition where every single communication to do with prorogation is being sought and it takes a coach and horses through our data protection legislation."
Refusing to take interventions from opposition backbenchers, Mr Gove added: "Their desire to rifle through private correspondences of advisers is to set aside legal precedent and the rights of citizens."
On Operation Yellowhammer, Mr Gove said: "The Government is absolutely committed to sharing with this House as much as we can."