Those interviewed referred to their experiences from the time of their arrest to their transfer to the Shin Beth internal security service for interrogation.
Sixty-seven per cent of those surveyed said they were subjected to "beatings, painful binding, swearing, humiliation and denial of basic needs".
"All signs point to the fact that these methods are employed according to set regulations and receive prior authorisation"
B'Tselem and the HaMoked Centre for the Defence of the Individual report
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The report said such measures "are defined by international law as ill-treatment and may reach the level of torture".
But the most severe treatment was meted out to "ticking bombs", detainees thought to possess information that could prevent attacks, the report said.
Some of those interviewed by the rights groups said they were deprived of sleep for more than 24 hours and beaten by security officers.
Other practices highlighted by the report include painful stretching of the body and bending the backs of detainees in an arch when in a sitting position.
The rights groups concluded that such treatment was carried out "under the auspices" of Israel's law enforcement system.
"All signs point to the fact that these methods are employed according to set regulations and receive prior authorisation," they concluded.
B'Tselem and HaMoked said that while the 73 Palestinians interviewed are "not a representative sample, it does provide a valid indication of the frequency of the reported phenomena".
The groups called on Shin Beth to stop using interrogation techniques "that injure the dignity or physical integrity" of detainees, urging the passage of legislation to ban them.
Israel's justice ministry said in a statement that the report was "based on a non-representative sample that was apparently chosen in an ill manner with a view to altering reality".
"The role of the Shin Beth is to ensure state security and to prevent illegal activities. To achieve these goals, it interrogates people suspected of terrorist activities."
Al Jazeera sought a further response to the report from Israel's justice ministry but no representatives were available.
Israel currently holds more than 9,000 Palestinians on charges of endangering state security, according to official figures.