Lee becomes the seventh player to sign up to an NDC which ensures he will remain with his chosen Region and stay under the umbrella of the Welsh Rugby Union.
He joins Sam Warburton, Dan Lydiate, Tyler Morgan, Hallam Amos, Rhodri Jones and Jake Ball on the current list of NDC players.
The Wales Head Coach, Warren Gatland, said: “Samson has developed rapidly and proven his ability in a position where we continue build strength in depth.
“His performances for the Scarlets and Wales have shown how he is a quick learner who understands the requirements of the role and the demands on a modern tight head.”
Welsh Rugby Union, Roger Lewis, added: “Samson is a great example of the kind of player who can emerge from our development pathway.
“He has achieved international success at a very young age for a tight-head prop forward and will undoubtedly continue to improve under the expert guidance he will get with a National Dual Contract.
“We are all delighted with the calibre of player we have signing up and all of Welsh rugby will feel the benefit of this system for years to come.”
Samson Lee said: “This was an easy decision for me, a National Dual Contract is the best of both worlds.
“It allows me to commit to the Scarlets, where I’m enjoying my rugby and where I feel at home, but it also hopefully allows for exciting times ahead with Wales.
“I hope I can continue to repay the faith placed in me by both by the Scarlets and the WRU coaches on the pitch and am delighted that I will be attempting to do so at Parc y Scarlets for the foreseeable future.”
Scarlets Head Coach Wayne Pivac said: “Samson has virtually put himself up there as a top-class international tight-head. Having confirmed that Ken Owens and Liam Williams have both signed new contracts with the region and Rhodri Jones signed up to an NDC we’re are pleased to see another of our international players committing his future to Wales and the region.”
Samson Lee was a member of the Wales U20 team during the Six Nations Championship in 2012 and also played in the IRB Junior World Championships that year in South Africa.
He won his first senior cap as a replacement against Argentina in 2013 and has now won nine caps for Wales, all at tight head.