Financial news agency Bloomberg reported on Tuesday that Saudi Arabia had sent a letter to an Abu Dhabi bank saying it had not approved the line crossing its territory.
The pipeline company said in a statement: "Dolphin Energy has not received any objection or protest from any country concerning the pipeline project that runs exclusively within the maritime areas of the states of the United Arab Emirates and Qatar."
A Gulf source told Reuters: "A project of this size and partners of this calibre cannot be agreed upon without first checking all legal and related documents."
Dolphin Energy is 51%-owned by Mubadala Development Company, an investment vehicle of the government of Abu Dhabi, and France's Total, and US Occidental Petroleum hold 24.5% each.
Dolphin said the pipeline, part of a $3.5 billion project, would be completed within a few weeks.
Gulf neighbours Saudi Arabia and Qatar have strained political relations over a number of issues.
Riyadh has objected to the construction of another gas pipeline from Qatar to Kuwait, and Qatar's oil minister has said that the project had been scrapped for that reason.
There is also a disagreement between Saudi Arabia and the UAE, under which the United Arab Emirates ceded to Saudi Arabia a strip of land linking the UAE and Qatar.
Abu Dhabi has said it wants to amend the pact.
The National Bank of Abu Dhabi, which Bloomberg said had received the Saudi memo, declined to comment.
The Dolphin gas project aims to pump an initial two billion cubic feet a day of natural gas from Qatar's giant North Field in the Gulf to buyers in the UAE.
Dolphin has already started to supply natural gas to Fujairah and Ras al-Khaimah emirates through a pipeline in the UAE.