The interior ministry said Mariam Koofi, a member of parliament from the northeastern province of Takhar, was shot in Kabul by a member of the security forces following an argument.
It said police have detained a suspect and are investigating the motive behind the attack.
But her sister Fawzia Koofi, who is also a member of parliament and a prominent defender of women's rights, said she was not certain who the attacker was.
"I am not sure who may have been behind this attack, and I hope the interior ministry takes serious actions to punish the attacker," she said.
Fawzia Koofi said shots were fired at her sister's car, hitting her in the leg once and her bodyguard twice. None of the injuries are life-threatening, said Fawzia.
Afghanistan's parliament reserves just over a quarter of its seats for women, who are active participants particularly on rights issues.
The attack comes as officials count votes from the April 5 election to choose a successor to President Hamid Karzai.
Early results suggest former foreign minister Abdullah Abdullah, runner up in the 2009 presidential poll, is leading his closest rival Ashraf Ghani, but a run-off is likely.
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