Several Niki flights scheduled for Thursday have been cancelled but those cancellations were long-standing and unrelated to any insolvency, a Vienna Airport spokesman said.
The European Commission said Wednesday that Lufthansa's move was "regrettable" and that withdrawing the bid completely "was not the only possible outcome".
Lufthansa had said it would now stop financing the airline, which it had been keeping afloat with about 10 million euros a week since August, Bloomberg News reported.
The European Commission called the current uncertainty for Niki employees and passengers "regrettable", and said it resulted from Air Berlin's insolvency, as well as Lufthansa's decision to drop the Austrian carrier from its proposed deal.
Lufthansa had already offered to give up numerous precious takeoff and landing slots it originally wanted under the deal.
Niki said earlier that it had applied to open insolvency proceedings following Lufthansa's announcement that it had "informed Air Berlin and its insolvency managers that it will pursue the planned transaction without the purchase of Niki".
Lufthansa was ready to transfer some of Niki's landing rights to leisure-travel operators Thomas Cook Group and TUI to satisfy European Union regulators, people familiar with the plans said on Tuesday.
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Aside from Lufthansa, Niki attracted bids from International Airlines Group (IAG) and Thomas Cook.
The German government had been expecting to use the sale proceeds as repayment for a 150 million euros bridge loan it awarded to Air Berlin to keep it flying after it filed for insolvency protection.
The EU said it will continue to review Lufthansa's takeover of LGW.
The German government said it regrets the EU's stance and will do everything it can to limit the damage to taxpayers.
Easyjet proposed to acquire certain assets and rights held by Air Berlin as part of its previous operations at Berlin Tegel airport, including landing and take-off permission at a specific date and time at Tegel airport and at some destination airports, according to an EU?statement.
Shares in Easyjet were down 0.1% at 1,438.00 pence Tuesday. That would leave the German government almost 100 million euros short.