The 3,500-year-old filigree flacon bears the name of Hatshepsut, an 18th-dynasty pharaoh who ruled from around 1479 BC.
Michael Hoveler-Muller, the museum's curator, said: "The desiccated residues of a fluid can be clearly discerned in the x-ray photographs... Our pharmacologists are now going to analyze this sediment".
"We think it probable that one constituent was incense - the scent of the gods."
He said that Hatshepsut used perfume to demonstrate her power.
Hatshepsut, best known to modern visitors to Egypt for her spectacular mortuary temple built into the bottom of a cliff near the Valley of the Kings, ruled in place of her son Thutmose III, for around 22 years.
"She systematically kept Thutmose out of power", according to Michael Hoveler-Muller.
During her regency, Haptshepsut undertook an expedition to Punt, the modern-day Eritrea. The expedition is believed to have brought back whole incense plants, which Hatshepsut then had planted in the vicinity of her funerary temple.