Individual income tax collections were 22 percent lower than expected for the month of May.
A House committee has inserted the Amazon language into an unrelated bill, in an attempt to keep it alive for negotiations.
Overall revenues were boosted by a surge in individual income tax collections, which came in more than $70 million ahead.
January revenues were higher than predicted, but sales tax revenues are falling short of predictions for this fiscal year.
Most new state laws take effect at the start of the fiscal year in July, but there are exceptions.
Traditional stores say e-commerce has an unfair advantage as consumers are exempt from paying sales tax on purchases from out of state.
Indiana is considering banning "sales tax zappers," computer programs that help business avoid paying sales taxes.
A poll from the Indiana Merchants for Tax Fairness shows 61 percent of Hoosiers say the same tax should be payed for local and online purchases.
Senator Greg Walker's bill would have gas distributors collect gasoline sales tax when they deliver shipments to local gas stations.
With the deal, Indiana becomes the fourth state in which Amazon will collect an online sales tax.