Members of the Rail, Maritime and Transport (RMT) union will vote on whether to launch campaigns of action.
The disputes involve this year's pay deal for directly employed staff and a row over wages for employees at facilities company Interserve.
Transport for London (TfL) urged the parties involved to resolve the issues.
RMT general secretary Mick Cash said the union planned to send a "clear message to management".
The union said the results of the ballot were due on 12 May.
TfL director Rory O'Neill, said: "This is a dispute between the RMT leadership and KeolisAmey Docklands and Interserve who employ the staff concerned.
"We urge all parties to sit down and talk through the issues to try and resolve them as soon as possible."
KeolisAmey Docklands, who operate and maintain the DLR, said the strike action was "unnecessary".
Kevin Thomas, managing director of KeolisAmey Docklands, said: "We are disappointed that the RMT union are balloting our employees, particularly as the pay offer reflects the requests received from the RMT."
A spokesman for Interserve said: "We have been in discussion with the union and employees so we are disappointed that strike action is being considered.
"We will continue to work closely with union and staff representatives to try and reach an agreement that is acceptable to everyone."
Workers on the Docklands Light Railway (DLR) are being balloted for strike action over two separate disputes.