CLEARWATER — Two months after the Church of Scientology lost out to the city on buying a crucial downtown property it needed for its campus, church leaders are now negotiating a land swap to fulfill both parties' redevelopment needs.

The City Council is scheduled June 14 to vote on whether to trade three city-owned properties, two being small parcels around the footprint of the proposed L. Ron Hubbard Hall at S Fort Harrison Avenue and Court Street, in exchange for a vacant lot east of downtown the city needs for parking for the retail portion of the Nolen apartment complex.

Scientology is under contract to buy the vacant lot adjacent to the Nolen for $625,000 from a company managed by developer Guy Bonneville with an agreement to then swap the property for the three city parcels, according to the contract.

Community Redevelopment Agency director Seth Taylor said when the city inquired about buying the lot directly from Bonneville's company in September, Bonneville conveyed he would sell the lot to the city only for "well above the assessed value."

When reached by the Times Tuesday, Bonneville declined to comment on the negotiations or whether he offered Scientology a better deal than the city. Bonneville is also the manager of his father-in-law's company that owns the Times Clearwater bureau building at 1130 Cleveland St.

Along with the two parcels surrounding the proposed L. Ron Hubbard Hall site in the land swap, Scientology would also acquire acquire nine parking spaces on Watterson Avenue which abut the northwest portion of the parking garage at 28 N Garden Ave..

City Manager Bill Horne said the land swap would save taxpayers money because the value of the three parcels is far below the price of what the city would pay if it bought the vacant lot for the Nolen directly through Bonneville at his inflated price.

The value of the city's three parcels total $425,000, according to appraisals ordered by the city in February. The city also obtained an appraisal of Bonneville's vacant lot adjacent to the Nolen, which is valued at $600,000.

"We're making what we believe to be the best business decision," Horne said. "I realize there's a lot of people that are going to try to interpret what's going on to mean all types of different things. But the church had been interested in the city properties for a while and we found a good way to address what our needs are and what they wanted. We don't really have an overarching need for those parcels."

The City Council was scheduled to discuss the land swap at its work session Tuesday, but Horne and Taylor said the item was pulled because church officials hadn't returned their calls or emails for two months and they were unclear of the status of the deal. The silence followed the city's April 20 purchase of a 1.4-acre vacant lot from the Clearwater Marine Aquarium for $4.25 million. The church had offered the aquarium $15 million for the site, which borders its 13-story Oak Cove religious retreat and is across the street from City Hall.

Horne said Scientology spokesman Ben Shaw called him Tuesday after the city's work session to arrange a meeting.

In a statement to the Times, Shaw on Tuesday said church legal counsel had been "in regular contact" with the city attorney's office, but he did not answer questions about why church officials stopped communicating with Horne and Taylor.

"I don't think we have a different perspective than the City," Shaw said. "There are a few small parcels we need to complete our event hall/convention center and park, and we've worked with the city to facilitate a trade for property they need."

Scientology proposed the 3,500-seat auditorium in the late 1990s, but the church has not submitted plans to the city for construction. Shaw said Tuesday it "has been designed and architectural plans/construction documents are in progress."

The church owns more than $260 million in property under its name in Clearwater, in addition to $26 million of downtown real estate it bought earlier this year through shell companies. In March, Scientology leader David Miscavige proposed bankrolling a facade overhaul of Cleveland Street, recruiting high end retail to empty storefronts and building an entertainment complex with actor Tom Cruise on the contingency the city step away and allow Scientology to buy the aquarium property.

Shaw has not responded to questions from the city about the church's next steps on the retail plan, Taylor said.

Mayor George Cretekos said he sees the importance of acquiring the lot adjacent to the Nolen, a complex of 257 apartments and retail expected to be completed this year being hailed by the city as a way to spur residential growth downtown.

But he said he's "not totally comfortable with the arrangement" with Scientology.

"I need to be convinced this is in the best interest of the city, and I haven't had those discussions with staff yet. ... One of the questions I had asked staff is if this property were important to us, why aren't we buying (directly from Bonneville)?" Cretekos said. "Why are we having to go through an intermediary?

Contact Tracey McManus at tmcmanus@tampabay.com or (727) 445-4151. Follow @TroMcManus.

Editor's note: This article has been changed to reflection the following correction — Among the parcels to change hands in a proposed land swap between the city of Clearwater and the church of Scientology are nine parking spaces on Watterson Avenue that abut the northwest portion of the parking garage at 28 N Garden Ave. A June 2 article incorrectly described the property to be swapped.