The AFPs' 1.97tn-peso (US$823mn) offer was below the 90% minimum price set by the government.
The government will now move to another stage of the process in which Ecogas will be offered to other bidders.
Last July, the government awarded the tender for a 97.2% stake in the investment vehicle for Ecogas - called Transportadora de Gas del Interior (TGI) - to the AFPs for 750bn pesos.
These funds will be returned to the AFPs, deputy mines and energy minister Manuel Maiguashca said.
The AFPs had already signed up Canadian pipeline company Enbridge (NYSE: ENB) as their strategic partner to administer the Ecogas network.
Colombia's six AFPs managed a combined 38.5tn pesos in assets at end-July.
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