That comes just days after a £51m funding package to take the mammoth tidal energy scheme, located between Caithness on the mainland and the Orkney Islands, forward was confirmed.
The latest deal for AIM-listed Atlantis means it will increase the initial number of turbines from four to six.
As a result the capacity of the array will rise from six megawatts to nine megawatts, which would be enough to power around 4,500 homes. The additional 1.5MW turbines will be installed on a foundation structure designed and built as of the ETI project.
In May 2012 ETI committed around £3.2m of funding for its Tidal Energy Converter Project which looked at the lifetime costs of tidal energy systems to try to develop technology to reduce the expenses involved. The foundation structure to be used at MeyGen came out of that first phase of research.
If the structure proves to be resilient in Scottish waters it could be rolled out to other tidal schemes. Work on installing the structure will begin this year with the two additional turbines operational in 2016 at the same time as the original four.
Tim Cornelius, Atlantis chief executive, said: "We are delighted that the ETI has selected Atlantis to continue to develop its marine project portfolio.
"Phase two of the Tidal Energy Converter project will see Atlantis expand its turbine array at the MeyGen site at Scotland and the scale of commercial marine energy generation in the UK.
"The ETI funded technologies to be designed and built as part of this project have the potential to substantially reduce the cost of energy of installed commercial turbines - improving the economics of tidal energy as part of the UK's energy mix."
The contracts for the installation and fabrication of the foundation structures have yet to be awarded.
Jonathan Wills, director of programme delivery at the ETI, said: "Results from the first phase of the project have provided a number of innovations across array system architectures and their operation and the potential impact in the cost of energy produced.
"In phase two we intend to demonstrate the most impactful of the innovations at a real site. The project should further enhance industry and investor confidence in tidal energy and help to unlock its potential as a serious contributor to future energy systems."
MeyGen could eventually have 269 turbines providing enough power for 175,000 homes.