The vote, reported by the state news agency IRNA, could help boost state coffers in the Islamic republic which has long depended on revenues from oil.
But since the plunge in international oil prices, the government has sought to tighten spending and raise taxes to offset the negative hit on state finances.
Revenues raised by taxing religious foundations and army-linked firms that control large parts of the economy could amount to 10 trillion rials (more than $350 million at the official exchange rate/300 million euros), budget committee member Mousalreza Servati had said in December.
The taxes would be raised from religious foundations and army-linked firms that control large parts of the economy and would be made to pay from the start of the fiscal year in March.
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The article approved by parliament, which is voting on the budget point by point, still has to be ratified by supreme leader Ayatollah Ali Khamenei.
If the legislation gets the go-ahead, it would target such giants as the Astan Qods Razavi foundation, which manages the shrine of Imam Reza in the northeastern city of Mashhad.
The shrine dedicated to the eighth Shiite imam draws million of pilgrims each year, but was exempted from paying tax by Ayatollah Ruhollah Khomeini, founder of the Islamic republic.
The foundation has also interests in mining, industry, agriculture and construction, according to Tasnim news agency quoting foundation official Gholam Reza Parandeh.
Another group that could be affected would be EIKO, which the United States says is a network of 40 firms run by the office of the supreme leader and in control of billions of dollars in investments.
Religious foundations benefit from donations as their main source of finance, and part of the taxes raised could be returned to them to bolster their budgets.