More than 50% of these firms also said they have no plans to rectify this situation within a year.
The survey was conducted by software company Ilog and supply chain professionals' magazine Apics. Researchers quizzed 120 executives - most employed by companies with a turnover in excess of $10m (£6.7m)- including 32 from Fortune 500 businesses.
Commenting on the findings, Steve Banker, director of supply chain research at manufacturing IT analyst firm ARC Consulting, said, "The ideal everyone is aiming for is robust collaboration with near real-time, automated exchange of information between partners.
"But at present there is a lack of standardisation of basic data such as part numbers and a lack of standardisation of data formats within EDI and with the Balkanisation of XML schemas which is taking place."
Of the 50% of all respondents who said that their supply chain systems were not synchronised with partners, 45% said they were using different software to other businesses in the chain.
The biggest obstacle identified as standing in the way of synchronisation was said by 37% of respondents to be a lack of a standardised IT platform and, by 53%, the lack of visibility of data between partners.