Soldiers sent the man toward a house where Palestinian fighters were holed up to persuade them to come out, a violation of army regulations, the announcement said.
The military said that it had disciplined another officer who ordered an airstrike near a mosque in Beit Lahiya, an attack that killed at least 15 civilians and wounded 40.
The military prosecutor also ordered a new investigation into the deaths of two dozen members of a family who were ordered by troops into a building that was shelled later in the fighting.
Around 100 members of the Samouni family were in their home in Zaitun when it came under Israeli bombing, killing 26 of them.
However, the military also said it was dismissing dozens of other incidents, many of which were raised in the UN Goldstone report on alleged war crimes during the conflict, the AFP news agency reported.
Israel's war on Gaza, which began at the end of 2008, killed around 1,400 Palestinians and 13 Israelis.
The announcement of the indictment against the soldier came hours ahead of a meeting between Binyamin Netanyahu, the Israeli prime minister, and Barack Obama, the US president, at the White House.
Sherine Tadros, Al Jazeera's correspondent in Jerusalem, said that if found guilty the soldier facing manslaughter charges could be sentenced up to 30 years in jail.
She said the case centred on a mother and daughter who were told, along with the rest of their family, to leave their house and head to the centre of Gaza city for safety.
"When they left their house with another 28 members of their family and their friends, 20 of whom were children, they were carrying white flags trying to tell the Israeli soldiers that they come in peace.
"Now after that an Israeli soldier started firing shots at the crowd and unfortunately two woman - a mother and child were killed.
"There are many questions that arise from this indictment - not least why it's taken about two years to investigate this and bring these charges to the soldiers involved."
The army said Palestinian witnesses and dozens of soldiers had been questioned during its internal investigation, but it had "found gaps between the testimonies given by the soldiers and those given by Palestinians".
"This fact made it impossible to make a criminal connection between the described incident according to Palestinian testimonies and to that described by the soldiers," it said.
However, the decision to charge the soldier with manslaughter was "based on evidence that the soldier, who was serving as a designated marksman, deliberately targeted an individual walking with a group of people waving a white flag without being ordered or authorised to do so," the army said.