The products would still be available over the counter, Larson's Pharmacy owner Paul Larson said.
A display in the shop would show customers what was available.
The pharmacy door was smashed, after a failed attempt to break the lock, about 1.30am.
A small amount of pseudoephedrine, the pharmacy's whole stock, was taken, Mr Larson said.
Prime Minister John Key wants a ban on over-the-counter sales of pseudoephedrine in a bid to combat the methamphetamine (P) epidemic.
Ministry of Health media relations senior adviser Karalyn van Deursen said legislation banning over-the-counter sales of pseudoephedrine and ephedrine was due before Parliament shortly.
Mr Larson said moving the stock to the back room was a logical step.
"It makes sense ... it's inconvenient to customers, but to save the inconvenience of burglary, we have to do this."
Sergeant Ed Baker said police had not arrested anyone for the burglary.
Closed circuit television in the pharmacy revealed there was one intruder, but the quality of the footage was not high.
A witness saw a vehicle leaving, but police did not have a good description of it, he said.
