An army spokesman would not provide further details on the investigation.
B'Tselem said in one incident, Israeli soldiers searching for fighters ordered an 11-year-old Palestinian girl to lead them into a house one night.
Jihan Daadush said the soldiers threatened to arrest her unless she led them to a nearby house.
"Three soldiers walked behind me. When we reached the house, there were a lot of soldiers. The soldiers ordered me to go inside the house and I went inside."
B'Tselem said Jihan told them the soldiers asked about the rooms of the house, then two of them returned her to her home. The report did not say whether troops found any fighters inside.
The girl was told to not to tell anyone about the incident: "I was afraid they would kill me or put me in jail. I am still afraid the soldiers will invade the city again and take me away," she said.
Jessica Montell, the executive director of B'Tselem told Al Jazeera: "It's the first time that we're seeing young children, and an 11-year-old girl being used in this way".
"It's terrifying experience for anyone, even adults who've gone through this tell us of the fear," she said.
Television footage also showed Israeli soldiers apparently forcing a young Palestinian man to walk ahead of them into a house.
Supreme court ban
David Chater, Al Jazeera's correspondent in Jerusalem said in this case Israei's hand appeared to have been forced by the fact that some incidents had been caught on camera, and that there may be many more cases which are going unreported.
B'Tselem said the evidence it had collected showed the the 'human shields' were given tasks that "undoubtedly included an element of danger and it seems clear that the soldiers were aware of this".
In 2005 Israel's supreme court banned the practice of using Palestinian civilians as human shields to search homes for explosives or fighters in advance of soldiers.
The Israeli army ended a five-day raid into Nablus on March 1.
During the incursion, troops shot dead a 42-year-old Palestinian civilian watching the raid from his rooftop.
Soldiers also detained 11 suspected fighters and claimed they had uncovered workshops used to manufacture explosive devices and bomb belts.