The Pakistan Federal Union of Journalists has decried the "shameful tactics" by a government.
As part of the black day, journalists plan to hold rallies, wear black armbands and raise black flags on press club buildings throughout the country, Mushtaq Minhas, president of the Islamabad press club, said.
"What happened yesterday was shameful and the darkest day in Pakistan's history," Minhas said, accusing the government of increasing intolerance towards independent media.
"Pakistan needs a military leader who can control both civil and possible military extremism"
Creative_person01, Islamabad, Pakistan
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The protests came a day after the supreme court dismissed several petitions challenging Musharraf's candidacy - a decision strongly opposed by lawyers and opposition groups.
Tariq Azim, Pakistan's junior information minister, and a legislator from a pro-Musharraf party were injured in the melee, after receiving a few punches from protesters before being rescued by aides and police.
Minhas said the police have registered cases under anti-terrorism laws against several journalists implicating them in the attack on Azim. "We condemn this dictatorial tactic," he said.
Despite dwindling popularity and increasingly bitter opposition, Musharraf, a US ally, seems set to be re-elected.
The ruling coalition says it has the numbers it needs, and even the general's main challenger, retired judge Wajihuddin Ahmed, has admitted he doesn't have much of a chance.
The election commission approved only six of the 43 candidates, including Ahmed.
The opposition alliance has said its legislators would quit parliament on Tuesday to protest the general's candidacy, a move also aimed at depriving the election legitimacy.
Musharraf, who seized power in a 1999 coup, has pledged to give up his powerful post as army chief if he wins the election, but he has faced growing opposition since his failed attempt to oust Pakistan's chief justice in March.
He is also struggling to contain increasing violence and growing domestic political backlash against his close ties with Washington.