Both English Heritage and Historic Royal Palaces have produced documentation alleging that Farrells' original 26-storey tower impacted strategic views of the Tower of London.
However, a spokesperson for Farrells was insistent that, despite the setback, amended drawings would be produced in time for the scheme to go to planning committee next month.
The new development, if it wins the green light, would house reporters from some of the UK's most high profile newspaper operations, including The Times, The Sunand The News of the World.
Tower Hamlets council confirmed that information and drawings produced in September by the two complainants indicated that the scheme would have a negative impact on the setting of the Tower.
The architect subsequently agreed to amend the proposals, which have prompted 26 objections to date, to lessen these 'negative effects'.
These objections include those from local residents who have complained that Farrell's tower would block out their sunlight.
Farrell's original plans included proposals for two buildings - a 50,000m 2, 13-storey building and a 75,000m 2, 26-storey tower - along with a public square. The new development will house 3,000 News International staff.