Defra has chosen Tyneside ahead of Merseyside as the location for the headquarters of the Marine Management Organisation, a new body to regulate and manage the sea around England.
A bid to bring the MMO and up to 200 jobs to the region had been led by Mersey Maritime, a trade organisation, along with The Mersey Partnership, the inward investment agency. Tyneside beat five other shortlisted regions to win the relocation.
A statement from Defra said Tyneside's bid "won strong backing across the North East, and ministers decided the area had the right mix of environmental, business and academic marine interests."
Maritime minister, Huw Irranca-Davies, added: "Tyneside was chosen for several reasons, not least because of its broad range and good balance of marine interests. It has a working port, a busy local fishing industry, and businesses including offshore renewable energy development, all of which fit well with the MMO's role.
"All of the shortlisted locations made professional, well-presented bids and I thank everyone involved for their efforts and enthusiasm."
Dave Pendleton, business development director at Mersey Maritime, said: "It's a disappointing decision. We have yet to see the scores in each criteria or specific reasons why Tyneside was chosen. Everything that was said about Tyneside's economy and environment could be said about Merseyside and Liverpool's.
"We were very pleased with our bid and our team worked very hard to make the shortlist."