Aquind Ltd wants to lay cables through Portsmouth, Hampshire, to Normandy.
The MoD submitted a letter to the planning inspectorate after a delay in the project’s planning decision was announced in January.
An Aquind spokesperson said the company was “keen” to address the concerns “in good faith”.
The verdict now rests with Claire Coutinho, the secretary of state of energy security and net zero.
In its letter, the MoD stressed the need for further collaboration with the Department for Energy Security and Net Zero to address its concerns in a manner consistent with their “sensitive nature”.
It asked the government department to clarify the proposed process and allow both the MoD and Aquind to provide feedback, along with a six-week extension to prepare representations.
The MoD expressed reluctance to engage with Aquind recently due to the absence of an agreed process “which affords appropriate protection to MoD’s concerns”.
It added that it would keep this situation “under review” as it develops its evidence.
In October 2021, the BBC’s Panorama programme revealed that Aquind was part-owned by Russian-born former oil executive Victor Fedotov.
The company has donated more than £700,000 to 34 Conservative MPs since the Aquind project began.
In 2023, the government’s decision to refuse permission for the £1.2bn link was overturned in the High Court.
Aquind spokesperson Ben Iorio said it was disappointing that the “alleged concerns” were not outlined.
He said: “The manner of the MoD’s last-minute interference will have negative impacts on all proposed developments and marine users in and around Portsmouth, including renewable energy, interconnectors, fisheries and many others.”
He added that the company “remain ready and willing” to address the MoD’s planning-related questions.
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