The body which speaks for the 42 Church of England cathedrals said it has concerns that incense could be covered by the new Psychoactive Substances Bill.
The Bill would make all legal highs automatically illegal, rather than the current situation where each new drugs has to be dealt with individually.
But there's a fear this blanket coverage could mean things like incense would be criminalised.
Some things, like alcohol and caffeine, are officially excluded from the law but incense is not.
The Dean of Wakefield, the Very Revd Jonathan Greener, told The Telegraph: "We wouldn't want to see clergy committing illegal acts simply by carrying on something which the church has been doing for 2,000 years and indeed something the Egyptians used two and a half thousand years BC."
He added: "We think it is an oversight but we wanted to alert them to it before it became law and we had to campaign for a change in the law.
"I don't think the Government deliberately wants to take away the right of churches to use incense in worship, we've made this representation to try to make it one of the legitimate exceptions.
"In Wakefield we have used it in Sunday services since the 1930s.
"We have two services two services with incense, I actually tried to get rid of one of them and the congregation were up in arms."
Minister of State for Policing, Crime, Criminal Justice and Victims, Mike Penning, said: "The blanket ban covers psychoactive substances consumed for their psychoactive effects. As such, the use of incense in religious services will not be covered by the Bill."