Canterbury Cathedral and St Paul's Cathedral are two of many places of worship identified as buildings where evidence of cocaine use was found.
The Sun has reported that traces of the Class A drug have been found in a number of iconic religious buildings throughout the country, including in London, Birmingham, Manchester and Cambridge.
The newspaper's special investigation used swabs that it claimed were "95 per cent accurate", to find traces of drugs.
The 1971 Misuse of Drugs Act says that there is a minimum of 14 years in jail for allowing premises to be used for drug-related activities.
"Our probe comes after the General Synod, the Church's parliament, expressed concern on 'the extent of drug misuse at all levels of society,' " according to the paper.
Drug information analyst, Harry Shapiro, said that: "Many churches can be hired for events, where guests might choose to take drugs, and have publicly accessible toilets."
It has been reported that authorities at Canterbury Cathedral were "sorry" to hear of the alleged cocaine use in the bathrooms, but said that its toilets were available to around a million visitors every year.
Other churches contacted by the tabloid also stressed that their bathrooms were open to the public.
St Lenard's Church in Shoreditch, east London was named as allegedly having traces of drugs and a St Lenard's spokesperson said that it hosted Narcotics Anonymous groups and stressed that drug use was "tolerated" if it meant addicts came to seek help.
