Brigadier Nicky Moffat has handed in her notice after 26 years' service.
"The timing of her departure is a blow to ministers as they prepare to this week announce controversial plans to reduce the Army's manpower from 100,000 soldiers to 82,000 by 2020," the Daily Mail reported today.
Moffat, 50, stunned colleagues by announcing she was stepping down as the Armed Forces' head of pay and strategic manning at the Ministry of Defence.
The report said Moffat was widely tipped to become the first female general in British military history.
Another high-ranking officer, Brigadier Justin Maciejewski, the director of combat, is expected to follow suit by seeking voluntary redundancy.
According to reports, both had become disgruntled at the deep cuts and there is speculation that more high-profile resignations will follow.
"Brigadier Moffat yesterday denied these claims but gave no further explanation for her decision to leave," the report said.