New distribution channels are causing travel managers new problems including reduced compliance and the increased use of website by rogue travellers.
Many TMCs are also failing to integrate their GDS services with Internet inventory for hotels, rail and cars.
The problems have been unveiled in new research by the UK and Ireland Institute of Travel Management (ITM).
The 135 travel managers and procurement heads questioned by ITM said the use of low cost carriers was mainly to blame for the fall in compliance with company travel policies.
The research also found while most TMCs offered clients a combination of GDS and web inventories, 46% of TMCs had this "workaround" technology for air only.
One in five TMCs used only the GDS to service clients.
Paul Tilstone, ITM's executive director, said: "The internet provides more and better content and rates for hotels, car rental and other travel services than GDS and yet this is clearly not being offered to buyers by a substantial proportion of TMCs.
"Most managed travel programmes require the corporate, TMC, distribution systems and suppliers to work in harmony.
"Whilst in general this is very much the case, the massive changes to the distribution chain in recent years can sometimes undermine that harmony."
Two other long standing problems also emerged in the ITM research conducted by Argate Consulting.
52% of respondents believe that the relationship between the supplier and the agents still has a "significant influence" on fares offered to their companies.
The vast majority (99%) of travel managers and procurement heads questioned also believed that
airline loyalty schemes still influenced booking behaviour while the figure for those who thought for hotel schemes did the same was 90%.
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