The Welsh Government has also confirmed the stretch of the Heads of the Valleys road will miss its opening deadline this year and will not be fully complete until 2020.
Costain started work on the job in 2015.
Minister for Economy and Transport Ken States said the problems are on Section 2 where Costain is widening the road between Gilwern and Brynmawr within the steep sided and environmentally sensitive Clydach Gorge.
He said: “The project has experienced delays and cost increases due to difficulties experienced on site.
“Costain has highlighted that the primary reason for this is due to a complex construction solution required to address the geological feature that they have discovered in one particular location along the scheme.
“The solution required will impact on the construction costs and programme.
“I am obviously very disappointed by this news, however, my officials are working with Costain to deliver the project as soon as practically possible.”
The scheme had an original budget of £220m which was increased by £50m in 2017.
In June 2018 the Wales Audit Office began an audit of the project’s commercial position and an interim report is due soon.