Hull-based civil engineering firm Spencer Group has been awarded the contract to build two new border control posts on the Humber.
The new facilities will be constructed at Hull's King George Dock and the Humber Sea Terminal in Killingholme.
Associated British Ports (ABP) invited tenders last October when the contract was valued at £12m.
The government subsequently awarded ABP £9.9m towards the cost of building them.
They will provide inspection facilities for customs and Border Agency staff as well as port health officials dealing with imported goods from Europe, including live animals and fish.
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Documentation and physical checks are now required on imports following the UK's departure from the European Union under Brexit after decades of frictionless trade.
Shortly before the historic UK-EU trade deal was struck late last month, ministers announced a six-month "period of grace" for EU imports to be allowed through UK ports without being subject to checks.
The move was partly aimed at avoiding potential traffic congestion but was also the result of a lack of necessary infrastructrure at UK ports as well as a shortage of staff.
The design and build contract with Spencer Group requires both new border control posts to be ready for July 1 when the physical inspection of imported goods from the EU is due to start.
The company, which has its head office at Humber Quays next to the city's Marina, is one of the UK's largest independent family-owned civil engineering businesses.
Meanwhile, the Hull and Goole Port Health Authority has announced the appointment of a new deputy chief port health inspector as it gears up for the new imports regime.
Sally Johnson took up the new role this week having previously served as principal port health inspector for the authority.
Chief port health inspector Laurence Dettman said: "Sally is well known to many of our stakeholders as a most competent and reliable officer.
"I am certain that she will flourish in her new role and prove to be a key asset in meeting the many challenges faced by the authority, particularly with our ongoing preparation for the post-Brexit EU imports regime."
Based in Hessle Road, the authority is expecting to double its current nine-strong inspection team over the coming months to be able to meet increased workloads created by the new trading arrangements between the UK and the EU.