Justice P Bhavadasan issued the interim order after admitting the petition moved by the two officers -- Commodore Anand Balakrishnan and Lt Ajay Jaykrishnan.
The officers sought to quash proceedings against them in the complaint filed by the woman against her husband and his superior officers.
The court also directed the state and central government to inform them of their views.
In the petition, the officers also sought records leading to the FIR against them and to quash it.
The petitioners also pointed to inconsistencies in the locations and time of various incidents which had been mentioned in the complaint.
The complaint was malafide and intended to bring a bad name to the entire Navy, they submitted.
Meanwhile, the victim filed an impleading petition in the case.
The High Court had criticised police for "protecting" the higher Navy officials, while dismissing the anticipatory bail application filed by Lt Ravi Kiran, whose wife had filed the complaint.
Justice Kemal Pasha observed that it was a "serious matter" to be dealt with severely by police and a thorough investigation has to be carried out.
The charges of torture related to dowry issues were against her husband and his relatives.
The Navy had denied her charges, saying the complaint was the result of a "marital discord" and the charges against "superior officers" were "unfair.
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