Sisi congratulated Abe on his third term as prime minister of the Japanese government, stressing that this reflects the Japanese people's trust in him.
He wished Abe success in applying his policies.
Sisi said the Egyptian people and government appreciate Tokyo's support for Cairo over the past decades.
He said he is looking forward to further boosting cooperation between the two countries, particularly at the economic and development levels.
Egypt, he told reporters, is currently building its institutions, noting that will be completed once the parliamentary elections are conducted on March 21.
The polls are meant to meet the people's aspiration to achieve democracy, stability, justice and development.
Sisi said he invited Abe to take part in Egypt's economic conference due in Sharm el Sheikh in March.