The transport watchdog on Tuesday denied claims that it was planning to extend the Kalkara marina.
NGO Graffitti on Monday warned that the extension would see the marina taking over the creek, to the detriment of neighbours and other boat owners. It urged people to voice their objections.
Graffitti said an application was proposing a "staggering 334 berths" all around the creek, with "a significant number of berths catering for large boats".
On Tuesday the Nationalist Party criticised the government for not consulting anyone about the planned extension.
However, Transport Malta later said in a statement it was not planning any extension - it was solely looking into how to better organise the berths in the area.