The behavior of critical frequencies of ionospheric E and F2 layers (foE & foF2) along with minimum ionospheric frequency (fmin) is studied for solar minima of cycle 21 (1986), 22 (1996) and 23 (2008) over Karachi (24.95°N, 67.13°E), Pakistan. The station is located at the crest of equatorial ionization anomaly region. Beside seasonal differences, pronounced change in the values of frequencies is noted from one solar minimum to another solar minimum. A strong and direct correlation of foF2 with Smoothed Sunspot Number (SSN) and F10.7 cm solar flux is observed. In the minimum of cycle 23, reduction in foF2 is noted due to reduction of solar EUV as compared to other minima. Also disappearance of semi-annual variations in foF2 is noted in cycle 23 minimum. Unexpectedly higher values of foE and fmin are observed in minimum of cycle 23 as compared to other minima. It is difficult to explain this unusual behavior of fmin and foE along with disappearance of semi-annual variation in foF2. It is possible that during very low solar activity, thermospheric conditions are changed which in turn altered the ionosphere. Further investigation of atmosphere-ionosphere coupling is required to understand this complex behavior. On comparison of observed values with IRI-2016, higher deviations are observed in foE before noon hours while in case of foF2, large deviations are noted during daytime. The absence of foF2 semi-annual variation in cycle 23 is not reproduced by IRI-2016. It is suggested that IRI-2016 need some modification for extremely low solar activity condition.