Alexander & Baldwin would no longer be eligible to retain the rights to millions of gallons of water that for decades it’s diverted from Maui streams under amendments made to a hotly contested bill that was approved by the Senate Ways and Means Committee this week.

Ways and Means Chairwoman Jill Tokuda said she tweaked the language of House Bill 2501 so that it would apply only to 10 other water permit holders, including ranchers, farmers and utilities, throughout the state — and not A&B.

“We actually took them out of the bill,” Tokuda told the Honolulu Star-Advertiser on Tuesday.

However, it’s not clear whether members of the Senate Ways and Means Committee understood that when they voted 9-2 in favor of the bill during a hearing held Monday. Some committee members said afterward that they were under the impression that A&B would still be covered under the revisions.

“That’s a surprise to me,” Sen. Sam Slom said when told that Tokuda had changed the bill to exclude A&B. He voted yes on the bill, but with reservations.

He noted that committee members aren’t always given copies of amendments before a vote.

But the effect of the changes was clear to A&B officials, who have been pleading their case to lawmakers, arguing that without HB 2501 the water to 36,000 Upcountry residents could be cut off and their plans to switch their sugar cane fields to diversified agriculture jeopardized.

Chris Benjamin, A&B’s CEO and president, expressed disappointment in the changes but said he was glad that the measure would apply to other water permit holders.

“We have always maintained that this bill is needed by farmers and ranchers across the state, so in that sense it is a positive vote for agriculture,” he said in an emailed statement. “At the same time, (Monday’s) action eliminates much needed relief for the island of Maui, where … farmers and residents in Upcountry Maui and the future of agriculture in the central valley depend on the legislation as well. We are hopeful that the Legislature will recognize these needs are equally as deserving of this bill.”

He said that he was pleased that the bill was still alive, however, and open to “further discussions.”

The measure will likely be debated by House and Senate members later this month during conference committee, and could be amended to again include A&B.

House Bill 2501 was proposed at the urging of A&B after Circuit Judge Rhonda Nishimura ruled in January that the company’s four revocable water permits were invalid.

The state Board of Land and Natural Resources had been extending the one-year permits on a “holdover basis” for more than a dozen years while legal and administrative challenges to A&B’s request for a long-term lease were resolved.

Nishimura said that the extensions were inconsistent with the legislative intent of short-term permits.

A&B then approached lawmakers, urging them to put forward a bill that would allow the company to maintain rights to the water while it awaited a final decision by the Land Board on its long-term lease.

Since then a handful of other farmers, ranchers and utilities that for years have also held short-term water permits expressed concern that they too could be affected by the court ruling if the Land Board determined that they need to apply for long-term water leases. Opponents of the bill have said that these concerns are unrealistic and were being used by A&B supporters as a scare tactic to pressure lawmakers to pass the bill.

The requirements for obtaining a long-term lease are more stringent than what’s needed to acquire a short-term revocable permit. The leases require an environmental assessment; consultation with the state Department of Hawaiian Home Lands to see whether beneficiaries need the water for customary practices; and in some cases a conservation district use permit, according to testimony from the Department of Land and Natural Resources on the bill. Long-term leases also have to be competitively bid.

HB 2501 has elicited weeks of protest from Maui taro farmers, environmentalists and Native Hawaiian advocates who have been battling A&B over its stream diversions in East Maui for some 15 years. They’ve argued that the amount of water being diverted from streams is excessive, violates the water code and has harmed taro farming and water ecosystems.

However, Tokuda (D, Kailua-Kaneohe) was vague when pressed Tuesday about why she deleted A&B from the bill. “There’s no specific reason,” she said.

Tokuda said that the revisions were designed to protect other water permit holders that could end up being inadvertently affected by the A&B court ruling.

Specifically, Tokuda deleted language from the bill that made it applicable to water users that currently have applications for long-term leases pending before the Land Board. She said that the only company that has such a pending application is A&B. Tokuda said the bill would only apply to shot-term permit holders that sought a long-term lease after the bill went into effect.

“This actually does not help A&B,” she said.

Asked whether she felt that she had been clear enough about the intent of the amendments during the Monday hearing, Tokuda said, “Apparently, we didn’t make it clear enough.”

House Speaker Joe Souki (D, Waihee-Waiehu-Wailuku) declined to comment on the revised bill, referring questions to the Senate. The House has largely supported the bill. During a full floor vote, members voted 44-7 in favor of the measure, allowing it to pass over to the Senate.

Asked whether Senate members were potentially using the bill as a bargaining chip to negotiate with House members during conference committee, he said, “I don’t know.”