Police were called to the Royal Air Force (RAF) Bomber Command War Memorial in Green Park on Monday and found engravings on the monument covered with paint.
Similar graffiti was found at the Animals in War Memorial in Hyde Park.
Westminster City Council officers are assessing the damage caused to the two privately-funded monuments.
"We deplore any act of vandalism or graffiti that desecrates memorials put in place to honour those who fought for our country's freedom. We will do everything we can to clean and restore the memorials as swiftly as possible," said Councillor Ed Argar, the council's cabinet member for city management.
The Bomber Command memorial, which has a three-metre bronze structure of seven airmen returning from a bombing raid, commemorates 55,573 air crew who died in action during World War II.
The animal memorial includes two bronze mules, a horse and dog and the silhouettes of other animals that served in British, Commonwealth and Allied armed services carved into the stone wall of the edifice.
The incidents occurred on a day of confrontation in central London between members of far-right group the English Defence League (EDL) and anti-facism demonstrators.
About 1,000 EDL protesters chanted "Muslim killers off our streets" in reference to the killing of soldier Lee Rigby in Woolwich, south-east London, last week by Islamist extremists.
Meanwhile, the number of reported Islamophobic attacks since the murder has continued to rise dramatically across Britain.
Faith Matters, a charity which monitors anti-Muslim hatred in the UK, said the number of incidents in the past six days had risen to 193, including 10 attacks assaults on mosques.
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