Works at scenic Mġarr ix-Xini creek in Gozo were stopped twice because of pollution, the Environment and Resources Authority said on Sunday.
Times of Malta had featured photographs taken on Wednesday showing how the sea turned murky because of works on a quay.
The Gozo Ministry had told the newspaper that works were stopped after a screen preventing sea pollution was damaged.
ERA gave a different version on Sunday, saying no silt curtain was deployed and it stopped works on Thursday. Furthermore, the works did not comply with the conditions it had imposed through a Nature Permit which specified that an ecological monitor should be present on site.
Nonetheless, the contractor recommenced works and was stopped once again by ERA officials on Saturday.
"ERA warned the contractor that works cannot proceed until a full silt curtain was deployed. It has to be adequately sealed at the edges, it stressed.
The authority again imposed the presence of the ecological monitor on site.
.