The New York Police Department and fire department officials responded to the suspicious package -- which was later determined to be a backpack filled with children's toys.
Phillips responded to the tweet, saying "we'll send you the bill."
The cost of securing Trump's eponymous building on Fifth Avenue -- which served as his campaign headquarters as well as his home, and will continue to be a hub for the president-elect and his family well past Inauguration Day -- has been a touchy subject for New York officials ever since Trump was elected.
Protecting Trump, including security at Trump Tower, costs the city of New York about $500,000 per day, officials say.
NYPD Deputy Commissioner John Miller testified on Capitol Hill earlier this month, alongside New York City-area House Democrats calling for Congress to give the city $35 million to cover security expenses for Trump solely during the transition.
The ongoing tensions over costs makes instances like the partial evacuation on Tuesday a flashpoint for the issue.
Dan Scavino Jr., the director of social media and a Trump senior adviser, responded to Phillips, calling him "an embarrassment to the @NYCMayorsOffice & the amazing #NYPD."
The mayor's office isn't backing down from their fight for more funding coverage.
"Congress owes our City a lot of money for providing the president-elect with the security he requires. We’ve outlined these costs in detail. It’s our job to aggressively advocate for the NYPD and for City taxpayers, and we won’t back down from that responsibility," Mayor's office spokesman Austin Finan said.
De Blasio has previously said that the fight for funding "ain't over" and, in the latest change to the fluctuating security plan, his office also released an altered plan for the placement of the NYPD near Trump Tower in an effort to "improve congestion and allow for easier access to deliveries for businesses within the security perimeter all while maintaining the safety and security of Trump Tower."
NYPD Commissioner James O'Neill said today that he's "absolutley optimistic" that they will be reimbursed for the costs of an increased presence around Trump Tower and that the security plan is "evolving."
Even those involved acknowledge that this is likely not going to be the final time tensions flare.
While the situation at Trump Tower was unfolding Tuesday afternoon, Phillips tweeted that it "will be a common occurrence. Important everyone stays calm & listens to officers."
ABC News' Alex Mallin contributed to this report.