Dr John Sentamu, a longstanding campaigner on the issue, makes the appeal in today's Yorkshire Post in which he describes the sexual exploitation of victims to "modern day slavery".
Dr Sentamu said he believed the decision not to opt in to the directive meant the UK would damage its ability to influence co-ordinated EU policy on the problem - particularly in relation to sex trafficking.
He said: "Sex trafficking is nothing more than modern-day slavery.
"This is women being exploited, degraded and subjected to horrific risks solely for the gratification and economic greed of others.
"I am therefore stunned to learn that the Government are 'opting out' of an EU directive designed to tackle sex trafficking.
"Generally, I am no great supporter of European directives, because of the supremacy of our Parliament, but this seems to be a common-sense directive designed to co-ordinate European efforts to combat the trade in sex slaves."
Dr Sentamu said: "The Home Office stated this week that 'the Government will review the UK's position once the directive has been agreed'.
"I believe that position is seriously flawed."
The archbishop quoted International Labour Organisation figures to stress how 2.45 million people around the world are in forced labour as a result of people trafficking and 43% of these are involved in commercial sexual exploitation.
He said hundreds of thousands of people were being trafficked into or within the EU each year.
Former Labour Europe minister Denis MacShane has written to Deputy Prime Minister Nick Clegg urging the Government to reconsider its position on the directive, saying: "It is the wrong signal to send to the pimps and traffickers."
But the Government has defended its decision not to opt in to the directive at this stage.
The directive is aimed at co-ordinating efforts across EU countries and will allow the prosecution of offenders in one state for offences committed in others.
Earlier this week, the Home Office said: "While the draft directive will help improve the way other EU states combat trafficking, it will make very little difference to the way the UK tackles the problem as there are no further operational co-operation measures which we will benefit from.
"Opting in now would also require us to make mandatory the provisions which are currently discretionary in UK law.
"These steps would reduce the scope for professional discretion and flexibility and might divert already limited resources.
"The Government will review the UK's position once the directive has been agreed, and will continue to work constructively with European partners on matters of mutual interest.
"By not opting in now but reviewing our position when the directive is agreed, we can choose to benefit from being part of a directive that is helpful, but avoid being bound by measures that are against our interests."