Construction on the scheme started in 2017 and is now 70% complete.
The contractor is blaming the coronavirus pandemic for the move.
A spokesperson for Dragados UK said: “Dragados UK is proud of the progress achieved with this project but the Covid-19 emergency and other factors have meant that our involvement in the project has ended earlier than originally anticipated.
“We wish the project every success as it progresses towards completion”
Client the Aberdeen Harbour Board will take over responsibility for the site from June 15.
Procurement for the services required to complete the remaining 30% of work packages has already started.
Michelle Handforth, Chief Executive, said: “This year’s summer season was of critical importance to the Aberdeen Harbour expansion project, as we endeavoured to complete a series of major construction milestones and continued to address the rock removal challenges first identified in October last year.
“The interruption to the schedule as a result of the Covid-19 emergency has had the effect of greatly compounding those existing challenges.
“It is too early at this stage to confirm what impact this will have on the construction timeline, especially given current Covid-19 restrictions, but the intention for a phased opening, when safe to do so, remains unaffected”.
In line with Scottish Government Guidance, activities on site are currently restricted to essential site protection works, safety and security measures.