Patrick McLoughlin MP said the crossing would either be built next to the existing Dartford crossing or connect the M2 with the A13 and the M25 between junctions 29 and 30.
A third option was dropped in December.
Mr McLoughlin said the decision to develop both ideas would not delay the scheme.
"We are committed to a new lower Thames Crossing, but whichever location is chosen, it will have a big impact on people in the area and we must make the right decision," he said.
"This work will not delay the delivery of the crossing but allows us to choose the best option for local people and the region's economy, so that it helps boost transport links and economic growth."
The existing Dartford to Thurrock crossing, which consists of the QE2 Bridge and a tunnel, is used by 140,000 vehicles a day.
The transport secretary said despite the introduction of a new remote payment system called Dart Change in October 2014, it is expected that by 2025 traffic levels will be greater than the capacity of the existing crossing.
Two possible sites for a new crossing over the River Thames will be developed in further detail, the transport secretary has announced.