A spokesperson for the heritage authority told the AJ that it has taken issue with some of the details of the architect's designs, specifically their impact on the Grade II-listed complex.
But the project's client was quick to dampen speculation that the scheme would not go ahead as planned.
'It's just a sort of process,' said Jonathan Reekie, chief executive of Aldeburgh Productions, which is hoping to expand its facilities within the site. 'There are a number of issues which need to be addressed because it's a complex planning application,' he added.
The 9ha site is the most visited tourist destination in Suffolk, with half a million visitors a year.
Some of the Maltings buildings were converted into a concert hall for Aldeburgh Productions in the late 1960s. However, the majority of the mainly 19th Century and early 20th Century buildings are in a state of serious disrepair, according to Reekie.
The scheme will face planners over whether it will be granted listed building consent early on 4 January.