"This treatment prevents double tax benefits," according to the IRS notice, noting that its stance "is consistent with prior guidance" of the agency.

PPP loans are designed to help small businesses (with no more than 500 employees) retain employees by paying eight weeks of payroll costs, excluding salaries above $100,000. If businesses use 75% of loan proceeds for payroll purposes, retain their full-time employee headcount and don't cut salaries for any employee earning less than $100,000 by more than 25%, their loans can be forgiven. If they rehire recent laid-off employees by June 30, they can also qualify for loan forgiveness.

Businesses that have their loans forgiven under the program don't have to pay taxes on the forgiven loan amount.

"The issue isn't that the loan was forgiven but that you didn't have to claim as income the amount of forgiveness," which is not usually the case, explained Brian Hamburger, founder, president and CEO of MarketCounsel.

If those businesses were able to also deduct expenses like payroll and rent, they would be receiving triple, not double, tax benefits, said Hamburger. Also, said Hamburger, "If an expense is covered by a PPP loan, and that expense is later forgiven, then it's not an expense at all."

Leon LaBrecque, chief growth officer of the Sequoia Financial Group, said financial advisors "should absolutely consider PPP loans for their clients. I have been recommending them and many folks have gotten them. They are helping small businesses and nonprofits."