We have have a number of stainless steel lines to install but have found carbon contaimnation adjacent to the weld area, it seems like carbon brushers have been used. Can any one advise a suitable cleaning method bearing in mide the site has strict rules on chemicals being used and pickiling is not advisable as the pipe work is installed.
By "Carbon contamination" you mean "Contamination with trace amounts of carbon steel" 
The tiny amount of carbon steel was eroded off the tips of the wires in the wire-brush when the welder cleaned the flux and weld spatter from around the joint.
Your welder has violated procedure by using the wrong tool to clean the joint.  That makes all his work suspect.  Chemical cleaning is the only way to remove the traces of carbon steel(Forged Steel Valves). You said that pickling is not acceptable.  I spoke with one of my engineers and he described passivation.  There is a procedure in which the part is soaked in a boiling nitric acid solution, or another procedure in which the part is soaked in a warm solution of primarily citric acid. 
I only see three coices: 
1. You can convince the customer to accept the welds with surface contamination,
2. You can passivate the welds and demonstrate that they have become chemically compliant,
3. or you can scrap all the contaminated piping and start over.  

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